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[Cancer Research 63, 4805-4808, August 15, 2003]
© 2003 American Association for Cancer Research


Advances in Brief

Association of the CpG Island Methylator Phenotype with Family History of Cancer in Patients with Colorectal Cancer1

Marsha L. Frazier2, Lixuan Xi, Jihong Zong, Nancy Viscofsky, Asif Rashid, Elsie F. Wu, Patrick M. Lynch, Christopher I. Amos and Jean-Pierre J. Issa

Departments of Epidemiology [M. L. F., L. X., J. Z., N. V., E. F. W., C. I. A.], Pathology [A. R.], Gastrointestinal Oncology and Digestive Disease [P. M. L.], and Leukemia [J-P. J. I.], The University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030


    ABSTRACT
 Top
 ABSTRACT
 Introduction
 Materials and Methods
 Results
 Discussion
 REFERENCES
 
Methylation of promoter CpG islands in colorectal cancer (CRC) falls into two categories: age related and cancer specific. Most cancer-specific methylation at CpG islands occurs in a subset of cases that display the CpG island methylator phenotype (CIMP). The underlying cause of CIMP is not known. Using methylation-specific PCR, we studied 47 CRC patients for methylation at five loci to determine whether the methylation status of CpG islands is associated with family history of cancer. Four of the loci were differentially methylated between the CRC cases with a family history and those with no family history. Patients with methylation at all four loci were 14 times more likely to have a family history of cancer than patients with methylation at none of the four loci. These findings suggest that there may be a genetic component to CIMP in CRC.


    Introduction
 Top
 ABSTRACT
 Introduction
 Materials and Methods
 Results
 Discussion
 REFERENCES
 
CRC3 arises from a series of genetic alterations and/or epigenetic events. The epigenetic events include loss of imprinting as happens with insulin-like growth factor 2, or methylation of the promoter regions of genes, which results in silencing (1, 2, 3) . Silencing of the hMLH1 mismatch repair gene by hypermethylation of its 5' CpG island is found in most sporadic primary CRCs with MSI (3) . Toyota et al. (4) identified a CIMP in CRC where multiple tumor suppressor genes (including hMLH1) are inactivated by promoter hypermethylation (4) . In another study, Toyota et al. (5) examined 30 differentially methylated CpG islands in CRCs and normal appearing colonic mucosa. Most of the CpG islands displayed age-related methylation (type A), which was detected in tumors and some normal colonic tissues. A small proportion of the CpG islands was methylated only in CRCs (type C methylation), with no methylation being observed in normal mucosa. A group of 50 tumors was analyzed for CpG island methylation using eight of the CRC-specific loci. The tumors fell into two groups based on their frequency of methylation; those with high level methylation where each tumor displayed methylation; at three or more loci (CIMP+) and those where methylation was low (CIMP-), occurring at two or fewer loci with an average of 0.3 methylated loci/tumor.

The molecular basis for the CIMP is not known, but it may have an underlying genetic component. To determine whether there is evidence for this, we studied five loci (p16, Mint1, Mint2, Mint31, and hMLH1) with CpG islands. We selected these loci because they had been reported previously to be methylated in CRC but not in normal colonic mucosa (4) . We used adenocarcinomas from an unselected series of CRC patients to determine whether the methylation of any of these loci was associated with a family history of cancer. Patients were defined as having a family history of cancer if they had one or more first-degree relatives with cancer. We found a strong association between CIMP and family history of cancer.


    Materials and Methods
 Top
 ABSTRACT
 Introduction
 Materials and Methods
 Results
 Discussion
 REFERENCES
 
DNA Extraction from Tumors.
We studied 47 unselected colorectal carcinomas obtained from the Department of Pathology at The University of Texas M. D. Anderson Cancer Center. None of the cases were known to be germ-line mutation carriers for mismatch repair genes, which would indicate that they had HNPCC. After resection, the specimens were immediately examined by surgical pathologist for histological confirmation of adenocarcinoma. Patients gave informed consent in the collection of samples according to institutional and federal guidelines. All tissues were flash frozen on dry ice within 1 h of resection and maintained at -80°C until DNA was extracted.

Approximately one gram of frozen tissue from each tumor was pulverized with dry ice. The dry ice was allowed to sublime overnight, and then DNA was extracted as described by Chi et al. (6) .

Sodium Bisulfite Modification of DNA.
Sodium bisulfite modification of DNA was performed by a modification of the procedure described by Frommer et al. (7) . DNA (1–2 µg) was denatured in 0.2 M NaOH at 37°C for 10 min in 55 µl. The sample was then adjusted to a concentration of 0.5 mM hydroquinone and 2.6 M sodium bisulfite (pH 5.0), in 600 µl by using freshly prepared stock solutions. The reaction mixture was then layered with mineral oil and incubated at 50°C for 16 h. The modified DNA was desalted with a QIAEX II kit (Qiagen). DNA was then eluted with 50 µl of low TE buffer [10 mM Tris and 0.1 mM EDTA (pH 8.3)] and adjusted to 0.3 M NaOH for 5 min at room temperature with a 3 M stock solution of NaOH. One microgram of glycogen for molecular biology (Boehringer Mannheim) was then added as carrier, and the DNA was precipitated with 0.6 volumes of 10 M sodium acetate and three volumes of ethanol and then washed with 70% ethanol. The pellet was allowed to dry and then resuspended in 20 µl of low TE. A more detailed protocol can be found on the Internet.4

MSP.
The DNA methylation status of CpG islands in p16, Mint1, Mint2, Mint31, and hMLH1 was determined by MSP (8) . These loci were shown previously to be type C CpG islands (5) . The methylation status of specific CpG sites was determined by using bisulfite-modified DNA and PCR primers that were designed to specifically amplify unmethylated DNA and methylated DNA. The primers and MSP conditions for Mint1, Mint2, Mint31, and hMLH1 were described by On-On Chan et al. (9) . The primers for p16 were described previously by Herman et al. (8) .

The PCR products were subjected to electrophoresis on 6% acrylamide gels and visualized by ethidium bromide staining. The methylated and unmethylated DNA was quantified with an {alpha} Imager 2000 and Image Quant Software ({alpha} Innotech Corp., San Leandro, CA). The results were expressed as the percentages of methylation by determining the density of the methylated band relative to the sum of the densities of the methylated and unmethylated bands. Any locus showing >=10% methylation was considered positive because in normal tissue, these loci are <10% methylated (9) .

Assessment of MSI in Tumor Tissue.
MSI was assessed in each of the tumors by the microsatellite markers BAT25, BAT26, D2S123, D5S345, and D17S250 as described previously (10 , 11) . The tumors were classified as MSI-H if instability was observed at two or more of the five markers studied.

Statistical Analysis.
We tested each of the loci individually using {chi}2 analysis to determine whether there was a significant association between methylation at the locus and family history. Then the association between the number of methylated loci and family history was evaluated using Fisher’s exact test. The methylation status was recorded as one of two categories according to the number of methylated genes of each patient: (a) those having 0–2 methylated genes and (b) those having 3–4 methylated genes. Family history was categorized as either no family history (for the 15 patients without first-degree relatives with cancer) or having a family history of cancer in one or more first-degree relatives (for the 32 other patients). The Cochran-Armitage trend test was performed to test whether the proportion of patients having a family history of cancer increases as the number of methylated loci increases. Odds ratios and 95% confidence intervals were calculated by using logistic regression analysis.

The normality test was used to show that ages were normally distributed. The t test was used to compare differences in age between those with a family history and those without. The one-way ANOVA test was used to compare differences in age between those patients with methylation at 0–2 loci and no family history, those with methylation at 0–2 loci and family history, and those with methylation at 3–4 loci and family history.


    Results
 Top
 ABSTRACT
 Introduction
 Materials and Methods
 Results
 Discussion
 REFERENCES
 
Identification of Loci Preferentially Methylated in Cases with a Family History of Cancer.
We determined CpG island methylation at five loci and MSI in a series of 47 patients with CRC (Table 1)Citation . Methylation of the Mint2 locus was observed in a high proportion of the CRCs studied and nearly as common among those cases without family history (60%) as those with a family history (59%). Mint31, Mint1, and p16 were methylated less frequently in 40, 49, and 40% of the cases, respectively. They were preferentially methylated in CRCs from patients with a family history of cancer at frequencies of 47, 56, and 50%, respectively, relative to patients with no family history (27, 33, and 20%, respectively). hMLH1 was methylated in 9% of the tumors, and the methylation occurred exclusively in adenocarcinomas of patients with family history. This preferential distribution was not statistically significant for any of the loci when each was analyzed individually by {chi}2 analysis.


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Table 1 Methylation patterns for patients with or without a family history of CRC

 
Increasing Probability of a Family History with Increasing Numbers of Loci Methylated.
Using the four loci p16, Mint 1, Mint 31, and hMLH1 that were preferentially methylated in CRC cases with a family history of cancer, we determined the percentage of patients with or without family history having methylation at 0, 1, 2, 3, or 4 loci (Fig. 1)Citation .



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Fig. 1. Distribution of methylated loci (MINT31, MINT1, p16, and hMLH1) in CRC cases with and without a family history of cancer.

 
When patients were categorized as having either 0–2 loci methylated (CIMP-), or 3–4 loci methylated (CIMP+), Fisher’s exact test showed a statistically significant association of CIMP+ and family history of cancer (P = 0.04). The Cochran-Armitage test showed a significant increasing trend in the proportion of having family history as the number of methylated loci increased from 0–2 to 3–4 (P = 0.03).

Because the probability of having a family history of cancer increases with age, we evaluated whether the average ages of diagnosis in different patient groups were significantly different. The average age of all patients was 59 +/- 13.7 years. The normality test showed that the ages of diagnosis for patients with family history (n = 32) and without family history (n = 15) were normally distributed. The average ages of diagnosis for these two groups were 57.6 +/- 14.1 years and 62.2 +/- 12.8 years, respectively. The t test showed that there was no significant difference in age of diagnosis between these two groups (P = 0.29). The one-way ANOVA test showed that there was no significant difference (P = 0.44) in the average age of diagnosis for CIMP- patients with no family history (n = 15), CIMP- patients with family history (n = 24), and CIMP+ patients with family history (n = 8). The average ages were 62 +/- 12.8, 57 +/- 15.1, and 61 +/- 10.7 years, respectively.

We evaluated whether the number of methylated loci predicts family history status after adjusting for age of diagnosis using logistic regression analysis and found that patients were 1.9 times more likely to have a family history of cancer as the number of methylated loci increased by one (P = 0.04). The 95% confidence interval was 1.036–3.55. However, age at diagnosis is not statistically significant in predicting family history of cancer, with an odds ratio of 0.97 (P = 0.3). Patients with methylation at all four loci were 14 times more likely to have a family history of cancer than patients with no methylated loci.

Family History for the Patients with Tumors Having Methylation at All Four Loci.
One of the four patients with methylation at all four loci developed a poorly differentiated adenocarcinoma of the colon at age 67 and breast cancer at the age 64. Her father had CRC, and her sister had breast cancer. A second patient developed a poorly differentiated adenocarcinoma of the left colon at age 49 and a poorly differentiated adenocarcinoma of the right colon at age 52, and her father developed CRC at the age of 75. The third patient developed CRC at the age of 75, and her mother had breast cancer at the age of 65. The fourth patient had cancer of the vocal cord at age 61, prostate cancer at age 70, and a mucinous carcinoma of the right colon at age 71 and had a strong family history of cancer. His pedigree is shown in Fig. 2Citation . He had two brothers and one sister who developed extracolonic malignancies, and one of the brothers developed multiple primary cancers. Both of his parents had a family history of cancer, and his paternal grandmother had CRC. All four patients with methylation at all four loci were classified as MSI-H because they had MSI at two or more of the five microsatellites tested. Three of the patients had more than one primary cancer.



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Fig. 2. Pedigree of CRC patient with methylation at all four loci tested. The filled symbols indicate family members with cancer. Under the symbol is the family members number, and below that is the current age, the age at death if deceased, or a dash if these are unknown. Below that the cancer types are listed and in parentheses, that age at diagnosis. A dash indicates that the age at diagnosis is unknown.

 
Methylation in Extracolonic Malignancy of Patient with Methylator Phenotype.
We were able to obtain archival tissue from the vocal cord cancer from the patient whose pedigree is shown in Fig. 2Citation . DNA was isolated from this tumor, and it was subjected to MSP at each of the four loci, p16, Mint1, Mint31, and hMLH1. Two loci (p16 and Mint1) were methylated.


    Discussion
 Top
 ABSTRACT
 Introduction
 Materials and Methods
 Results
 Discussion
 REFERENCES
 
Four of the loci that we studied, p16, Mint1, Mint 31, and hMLH1, were methylated more frequently in CRC cases with a family history of cancer than in those without. Adenocarcinoma of the colon and breast were common among the family members of the patients with tumors having methylation at all four loci. One of the patients with methylation at all four loci in his CRC also had methylation at p16 and Mint1 in his vocal cord tumor, supporting the possibility of an underlying genetic component. That only two of the four loci were methylated in the vocal cord could be because the pathway of tumorigenesis varies from one tumor type to another, and therefore, the selective pressure for silencing of target genes during colorectal tumorigenesis is probably different from that for vocal cord tumors.

All four of the patients with methylation at the hMLH1 locus had the MSI-H phenotype. Eight patients had the MSI-H phenotype but no methylation at the hMLH1 locus. One of these eight patients met the Amsterdam criteria for HNPCC and had methylation at three of the four loci we examined but not at the hMLH1 locus. HNPCC is caused by germ-line mutations in mismatch repair genes. Although we have not yet been able to identify a germ-line mutation in a mismatch repair gene in this patient, such a mutation would explain the MSI-H phenotype. In addition, there would be no selective advantage to tumorigenesis for methylation to develop in the hMLH1 promoter region if the tumor had a defective mismatch repair pathway because of HNPCC. This patient may therefore have both the methylator phenotype and a germ-line mutation in a mismatch repair gene. Indeed, genetic predisposition to CIMP could be a modifying factor contributing to the penetrance of HNPCC.

Three other MSI-H patients with no methylation at the hMLH1 promoter had a first-degree relative with CRC and met the Amsterdam criteria for HNPCC, two developed CRC at early ages (36 and 45), and one developed CRC at the age of 59. It is therefore likely that these patients had HNPCC, and the MSI-H phenotype arose as a result of a germ-line mutation in a mismatch repair gene.

The number of our cases suspected of having HNPCC, MSI, or family history of cancer is higher in this study than what would be expected in a population-based study (12) . This is probably because U.T.M.D. Anderson Cancer Center is a referral hospital, and many CRC patients come here because of our focus on hereditary CRC. Therefore, although we report an association between CIMP+ and family history, it is important to note that the frequency of CIMP associated with CRC may therefore be over-represented in this study.

In hyperplastic polyposis, it has been shown that methylation in tumors displays a high degree of concordance within individuals, supporting the concept of a shared etiology, such as genetic predisposition (9) . In another study on colorectal adenoma patients, methylation at the hMLH1 promoter was more frequent among those patients with a single first-degree relative with CRC than those without such a history (13) .

Recently, Gazzoli et al. (14) reported a series of 48 patients with CRC meeting the (a) Amsterdam; (b) modified Amsterdam; (c) HNPCC like; or (d) Bethesda criteria. One of these patients had an MSI-H tumor, no detectable germ-line mutation in hMSH2, hMLH1, or hMSH6, and displayed methylation of the hMLH1 promoter region in DNA from his blood and tumor. DNA isolated from blood was available from two of our patients displaying methylation at all four loci. To determine whether methylation was common in DNA isolated from blood of patients with CIMP, both samples were analyzed for methylation at the hMLH1 promoter and found to be negative (data not shown).

Lifestyle factors such as alcohol consumption and smoking have been reported to be associated with a substantially increased risk for MSI-H CRC in a population-based case control study (15 , 16) . Methylation of the hMLH1 promoter was not reported in this study. However, with the exception of HNPCC-associated MSI, most of the MSI in CRC is thought to be attributable to methylation of the hMLH1 promoter (3) , and therefore, it is likely that this association between these lifestyle factors and MSI is because of methylation of the hMLH1 promoter. One might speculate that these lifestyle factors are also risk factors for CIMP+ CRC in families where smoking and high levels of alcohol consumption occur. Additional studies are needed to evaluate how lifestyle factors, environmental factors, and genetic susceptibility might interact to cause CIMP+ tumors and influence risk for CRC. Families with CIMP+ CRC will be invaluable for elucidating the underlying mechanisms in the development of CIMP.


    ACKNOWLEDGMENTS
 
We thank Dr. Maureen Goode for her editorial comments.


    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 Grant CA70759 from the National Cancer Institute and by NIH Cancer Center Support Grant CA16672. Back

2 To whom requests for reprints should be addressed, at Department of Epidemiology, Unit 189, The University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030. E-mail: mlfrazier{at}mail.mdanderson.org Back

3 The abbreviations used are: CRC, colorectal cancer; MSI, Microsatellite instability; CIMP, CpG island methylator phenotype; MSP, methylation-specific PCR; MS1-H, microsatellite instability-high; HNPCC, hereditary nonpolyposis colorectal cancer. Back

4 Internet address: www3.mdanderson.org/leukemia/methylation. Back

Received 12/26/02. Revised 4/11/03. Accepted 6/23/03.


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 Results
 Discussion
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T Higuchi and J R Jass
My approach to serrated polyps of the colorectum
J. Clin. Pathol., July 1, 2004; 57(7): 682 - 686.
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