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[Cancer Research 61, 4541-4544, June 1, 2001]
© 2001 American Association for Cancer Research


Regular Articles

Extensive Somatic Microsatellite Mutations in Normal Human Tissue1

Susa Vilkki, Jen-Lan Tsao, Anu Loukola, Minna Pöyhönen, Outi Vierimaa, Riitta Herva, Lauri A. Aaltonen and Darryl Shibata2

Department of Medical Genetics, University of Helsinki, FIN-00014 Helsinki, Finland [S. V., A. L., L. A. A.]; Department of Pathology, Norris Cancer Center, University of Southern California School of Medicine, Los Angeles, California 90033 [J-L. T., D. S.]; Departments of Pathology [R. H.] and Clinical Genetics [O. V.], Oulu University Hospital, FIN-90220 Oulu, Finland; and The Family Federation of Finland, FIN-00101 Helsinki, Finland [M. P.]


    ABSTRACT
 Top
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
Microsatellite (MS) instability occurs in tumors with DNA mismatch repair (MMR) deficiencies but is typically absent in adjacent normal tissue. However, MS mutations have been observed in normal tissues from rare individuals with congenital MMR deficiencies. Autopsy tissues from a 4-year-old with congenital MMR deficiency (MLH1-/-) were examined for MS mutations. Insertions and deletions were observed in CA-repeat MS loci. Approximately 0.26 to 1.4 mutations per MS locus per cell were estimated to be present in normal heart, lymph node, kidney, and bladder epithelium. These findings illustrate that phenotypically normal MMR-deficient cells commonly accumulate MS mutations. Loss of MMR and the accumulation of some MS mutations may occur early in MMR-deficient tumor progression, even before a gatekeeper mutation.


    INTRODUCTION
 Top
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
Normal human tissues harbor somatic mutations at low frequencies. For example, HPRT mutation frequencies reach approximately 10-4 in normal adult epithelial cells (1) . Mutations in normal tissues can also be detected in some patients with cancer (2 , 3) but tumors generally contain many more mutations (4 , 5) . Mutation frequencies increase with histological progression (6) , which suggests that genomic instability increases with progression (7) .

Genetic progression is synonymous with histological progression because tumors are the only natural sources of cells with large numbers of somatic mutations. Although clonal expansion facilitates detection, mutations in normal cells may be rare because of high replication fidelity and efficient recognition and repair of DNA damage (4 , 5 , 8) . Cells with DNA damage often fail to progress through cell cycle checkpoints and may be eliminated through apoptosis (9) .

Rare individuals have congenital defects in MMR3 because of bi-allelic or dominant negative germ-line mutations (10, 11, 12) . Such individuals, similar to MMR-deficient mice (13) , are tumor prone but otherwise develop normally. Mutations in simple repeat sequences or MS loci, characteristic of MMR deficiencies (14) , are present in their phenotypically normal tissues (10, 11, 12) . Here, we identify another such individual and perform a quantitative mutation analysis to determine whether the large numbers of mutations expected to occur in the absence of MMR accumulate in the absence of tumorigenesis.


    MATERIALS AND METHODS
 Top
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
Patient.
An asymptomatic 4-year-old female died unexpectedly of hemorrhage caused by a glioma, and genotyping (15) revealed her to be homozygous for a germ-line exon 16 MLH1 deletion. Tissues saved at autopsy were brain, kidney, heart, liver, bladder, lymph node, and glioma.

MS Analysis.
DNA was extracted from fixed autopsy brain, kidney, heart, lymph node, and microdissected bladder epithelium. For controls, DNA was isolated from lymphocytes and fixed normal colon from MMR-proficient individuals. CA-repeat MS loci DXS556, 1060, and 453 were amplified using 42 cycles and incorporating 33dCTP during PCR (16) . The DNA was extensively diluted before PCR and ~30–70% of reactions had products that suggested that most products represented single molecules. Between 42 and 56 molecules were genotyped for each autopsy tissue at each locus. Frameshifts in the A-10 region of TGFBRII were assayed by dilution and PCR (17 , 18) of DNA isolated from peripheral blood lymphocytes.

Quantitative Analysis.
MS alleles were plotted as frequency size distributions. Variances were calculated for the unimodal distributions of DXS556, and separately for each of the modes of DXS1060 and DXS453. Assuming stepwise mutation and starting with germ-line-sized alleles in all of the cells, the variance of a MS frequency distribution is approximately equal to the average number of mutations at the locus (16) . For example, with a variance of 1, on average, each locus has mutated once, although there will be a distribution of allele sizes among cells. This analysis can count absolute numbers of single repeat unit changes, although counteracting stepwise additions and deletions will tend to return mutant alleles back to germ-line sizes. Numbers of division are estimated by: number of divisions = number of mutations ÷ mutation rate.


    RESULTS
 Top
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
Autopsy of an untreated, asymptomatic 4-year-old female revealed brain hemorrhage, caused by a glioma, and cafe au lait spots including multiple axillary freckles characteristic of neurofibromatosis type 1. No other abnormalities were found. Both parents had familial histories of HNPCC with heterozygous germ-line exon 16 MLH1 deletions. Genotyping revealed inheritance of the HNPCC mutation from both parents because the patient was homozygous (MLH1-/-) for the exon 16 deletion (Fig. 1)Citation .



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Fig. 1. MLH1 exon 16 deletion genotyping. Wild-type allele yields a 475-bp PCR fragment, whereas the mutant allele produces a 634-bp fragment. The 4-year-old patient (b) harbors a homozygous deletion of MLH1 exon 16 (MLH1-/-). Positive HNPCC (MLH1+/-, a, c–e) and wild-type (f) controls are illustrated.

 
DNA was extracted from normal heart, kidney, lymph node, and bladder epithelium. Other tissues such as the colon or the brain were unavailable, or their DNA was too degraded for analysis. Sizes of CA-repeat MS alleles were determined by dilution to essentially single copies followed by PCR (Fig. 2Citation ; Table 1Citation ). Somatic mutations were commonly present in the MLH1-/- autopsy tissues (15–32% mutant alleles) but not in MMR-proficient control tissues (<5% mutant alleles). Stepwise mutations lead to progressively broader allele distributions centered around germ-line sizes (16) . Consistent with stepwise mutation, allele frequency distribution modes (unimodal for DXS556 and bimodal for DXS1060 and DXS453) were identical between tissues and likely represent germ-line allele sizes (Fig. 3)Citation . Variances were between 0.26 and 1.4 and were similar among tissues (Table 1Citation ; Fig. 4aCitation ), which suggested approximately equal numbers of mutations because numbers of MS mutations are proportional to variances of MS mutation frequency distributions (16) . Frameshift mutations in the A-10 coding region of TGFBRII were not increased in lymphocytes compared with a MMR-proficient control individual when ~100 molecules were examined (Table 1)Citation .



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Fig. 2. Autoradiographs of DXS453 MS alleles from DNA diluted from normal MLH1-/- kidney (a) or MMR-proficient lymphocytes (b). {blacktriangleup}, mutant alleles; {triangleup}, germ-line alleles.

 

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Table 1 Mutation data

 


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Fig. 3. MS allele frequency distributions. a, distributions from normal tissues of the MLH1-/- autopsy. Circled, distribution modes allele sizes (likely represent germ-line alleles). b, comparisons with other MMR-deficient tissues; 41-day-old xenograft of the MLH1-/- colon cancer cell line HCT116 (data from Ref. 35 ), MMR-proficient male lymphocytes (no mutations), and a MLH1-/- HNPCC colon tumor (data from Ref. 16 ).

 


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Fig. 4. Variances of MS allele frequency distributions. a, variances of the MLH1-/- normal tissues. The variances for DXS1060 and DXS453 represent averages of their two distribution modes. b, variances of other MMR-deficient tissues. Variances of normal intestines of pms2-deficient mice increase with age (23) from 53 to 407 days.

 
For comparison, frequency distributions from MSI+ tumors are generally broader than from the MMR-deficient normal tissues (Fig. 3b)Citation . However, the MMR-deficient normal tissues contained greater numbers of MS mutations compared with a 47-day-old xenograft of the MMR-deficient tumor cell line HCT116 or intestines from a 53-day-old MMR-deficient (pms2-/-) mouse (Fig. 3b)Citation . By 1 year of age the variances of the repair-deficient murine intestines exceeded most of the variances observed in the normal autopsy tissues (Fig. 4b)Citation .


    DISCUSSION
 Top
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
Somatic MS mutations have been detected in normal tissues of individuals with congenital MMR deficiencies (10, 11, 12) . Here, we further analyze autopsy tissues of one such 4-year-old MLH1-deficient individual and demonstrate that large numbers of MS mutations are compatible with normal phenotypes. MS mutations are a function of cell division because slippage occurs during DNA replication (14) . Assuming stepwise MS mutation, allele frequency distributions estimate mutation numbers (16) . The observed variances (between 0.26 and 1.4) represent, on average, 0.26–1.4 mutations per MS locus per cell. Therefore, virtually all of the normal cells contained mutations considering the thousands of MS loci per genome. Assuming a MS mutation rate consistent with tissue culture studies (5 x 10-3 per division; Refs. 19 , 20 ), the cells divided about 52–280 times.

Mutations may be rare in normal tissues because cells with DNA damage can fail to progress through the cell cycle (9) . However, MLH1-deficient cell lines exhibit G2-M checkpoint deficiencies in response to agents that form mispairs (21) , which may allow MLH1-deficient normal cells to divide despite unrepaired slippage. In addition, DNA damage is less than the mutation burden because most base mispairs would be corrected after the next DNA replication. These somatic mutations are detectable by experimental comparisons, but a cell could not easily recognize a previously mispaired base. Many MS mutations could accumulate despite intact checkpoint mechanisms because damage during any single cell cycle may be below an activation threshold. For example, base substitution frequencies are similar regardless of p53 status (22) .

Although MSI+ tumors and these normal tissues both lack MLH1, MSI+ colorectal tumors have greater numbers of MS mutations (about 10 mutations per locus) and exhibit modal shifts from germ line (16) . More mutations in MSI+ tumors may simply reflect greater numbers of divisions between loss of MMR and tumor removal as MMR-deficient cells accumulate mutations with division (16 , 19 , 20 , 23) . The fewer numbers of mutations in the normal tissues are consistent with their lack of mitotic activity and the young age of death. Lymphocytes may undergo variable numbers of divisions, but the majority divide infrequently (24) . The only available epithelium came from the bladder, which is not characterized by high turnover (25) . Of note, frequencies of single-base alterations but not dinucleotide MS mutations vary with specific MMR component deficiencies (26) , and mutations inactivating p53 or leading to chromosomal instability and aneuploidy are rare in MSI+ colorectal cancers (6 , 27 , 28) .

Numbers of divisions should correlate with numbers of mutations in noncoding MS loci and coding loci. Tumor suppressor genes such as APC, TGFBRII, and BAX frequently have frameshift mutations characteristic of MMR deficiency in MSI+ tumors (18 , 29 , 30) . Base substitutions and short mononucleotide repeat deletions are increased ~100-fold with MMR deficiency (31 , 32) , but they would still be relatively rare, with mutation rates approximately 10-5 to 10-6 per division versus the 10-2 to 10-3 estimated for CA-repeat MS loci (19 , 20 , 33) . Consistent with these estimates, whereas CA-repeat mutations were between 0.26 and 1.4 per cell per locus, somatic mutations in the A-10 region of TGFBRII were not increased compared with MMR-proficient controls when ~100 molecules were examined.

A combination of mutations are needed for transformation of human cells (34) , and, therefore, some tumor mutations may accumulate in the absence of histological alterations or prior to a gatekeeper mutation (6) . Somatic mutations have been described in normal but presumably clonally expanded tissues adjacent to cancers (2 , 3) . The present study illustrates that large numbers of noncoding MS mutations can accumulate in normal tissues in the absence of tumorigenesis or abnormal clonal expansion. The prevalence and length of an occult period in which mutations accumulate before a gatekeeper mutation is an uncharacterized challenge. A molecular tumor clock analysis suggests that this interval can be long because the majority of somatic MS mutations may accumulate before clinically detectable tumorigenesis (16) .


    FOOTNOTES
 
The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked advertisement in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

1 Supported by National Cancer Institute Grant CA70858. Back

2 To whom requests for reprints should be addressed, at Department of Pathology, Norris Cancer Center, University of Southern California School of Medicine, Los Angeles, CA 90033. E-mail: dshibata{at}hsc.usc.edu Back

3 The abbreviations used are: MS, microsatellite; MMR, mismatch repair; HNPCC, hereditary nonpolyposis colorectal cancer; MSI+, mutator phenotype. Back

Received 11/ 3/00. Accepted 4/ 3/01.


    REFERENCES
 Top
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 

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