Chapter II. The Epigenetics of CRC - From Prognostics to Carcinogenesis
2.2 Methods
Patient eligibility
The target number of recruited patients with CRC was 320, and more than 30%
should be EOCRC. Patients who met the following inclusion criteria were eligible for
this study: (1) age ≥ 20 y/o, (2) cytologically or pathologically proven CRC and
adequate staging (American Joint Cancer Committee on Cancer, 7th edition) by
computed tomography, and (3) undergoing a colectomy surgery. The exclusion criteria
were that they received systemic chemotherapy or radiotherapy before colectomy.
Written informed consent was obtained from all patients before collecting the tumor
specimens. We also collected the patients’ clinical and pathological characteristics,
including age, sex, histology and grade of tumors, tumor location, the risk factors of
CRC, and BMI. The definition of these clinicopathologic variables is described below.
For age, the patients were categorized as age < 50 y/o and age ≥ 50 y/o. The histology
of tumors included the presence or absence of mucinous components, signet-ring cells,
and medullary histology, which were observed by microscopic examination. Mucinous
carcinoma was designated if more than 50% of the tumor volume was a mucinous
component. The tumor grade was classified into low and high grades. Tumors were
graded as a low grade if ≥ 95% of the tumor has glandular formation or MSI-high.
Otherwise, tumors were graded as a high grade. Tumor location was grouped into
right-sided and left-right-sided. Right-right-sided tumors were designated if the primary tumors were
located from the cecum to the splenic flexure of the transverse colon, and left-sided
tumors were located from descending colon to the rectum. The Institute Review Board
of National Taiwan University Hospital (NTUH) approved this study.
Risk factors
In this study, risk factors include first-degree family history for CRC, history of
colorectal polyp, DM, hyperlipidemia, BMI at diagnosis, pre-diagnosis use of NSAIDs,
and hormonal replacement therapy (HRT). These data were obtained from interviews
with the patients and the survey of the electronic chart of NTUH. The definitions of
these risk factors are described below. Patients with more than one first-degree family
member diagnosed with CRC were grouped into a group with a family history of CRC.
BMI at diagnosis was retrieved from a medical record. We categorized BMI into three
groups based on WHO criteria of 18–24.9, 25–29.9, and ≧30 kg/m2. We also
categorized BMI into two groups (< 27.5 and ≧ 27.5 kg/m2) according to the experts’
opinion for appropriate BMI in Asian populations from WHO expert consultation67. In
that report, a BMI of ≧ 27.5 kg/m2 was regarded as a high risk for public health.
Histories of DM and hyperlipidemia were determined according to self-reports and/or
the identification of the use of medication for these diseases. Pre-diagnosis NSAIDs use
was defined if two or more times per week in one month or longer within one year of
NSAIDs use was reported. Pre-diagnosis of HRT use was determined if six months or
longer of HRT use within one year was reported.
CIMP analysis
We used a QIAamp DNA formalin-fixed paraffin-embedded (FFPE) tissue kit to
extract genomic DNA from tumor specimens (Qiagen, Santa Clarita, CA, USA). Then
the genomic DNA was treated with sodium bisulfide according to the EZ DNA
Methylation Kit protocol (Zymo Research, Irvine, CA, USA). We evaluated the
methylation status of five loci: MINT1, MINT2, MINT31, p16, and MLH1 (classical
panel) using MethyLight assay, which was a probe-based, methylation-specific
real-time polymerase chain reaction technology. The primers used for the MethyLight study
are listed in Table 1. The methylation-independent Alu repeat was measured for
normalization control reaction. The methylation levels of five loci in tumor samples and
a constant reference sample were measured, and quantification analysis of DNA
methylation was performed. The percentage of methylated reference (PMR) of each
locus was calculated based on the equation proposed in a previous study as the
following: PMR = 100 × (methylated reaction / control reaction)sample / (methylated
reaction / control reaction)M.SssI-Reference. A PMR of > 10 was regarded as
hypermethylated49. Finally, CIMP-high tumors were determined if there were three or
more loci with a PMR of >10 identified. Otherwise, the tumors were determined as
CIMP-low/negative.
RAS/BRAF mutation analysis
We evaluated RAS (KRAS and NRAS) and BRAF mutations by PCR coupled with
Sanger’s sequencing method. The primers in this study covered exons 2, 3, and 4,
including codons 12, 13, and 61 of KRAS and NRAS, and covered exon 15 of BRAF.
After PCR, we used an automated ABI 3730 sequencer (Applied Biosystems, Foster
City, CA, USA) for direct sequencing.
MSI analysis
We used the MSI Analysis System (Promega Corp., Madison, WI, USA), a
PCR-based assay for detecting MSI, in five mononucleotide loci (NR-21, NR-24, MONO-27,
BAT-25, and BAT-26). Tumors were designated MSI-high if abnormal allele length
was identified in two or more loci. Otherwise, tumors were MSS.
Statistical analysis
The patient’s clinicopathological characteristics were presented as percentages and
frequencies. The association between CIMP-high CRC and clinicopathological
variables was estimated by logistic regression (Table 2), Fisher’s exact test, and
Chi-square test (Table 3 and Table 6). The association between risk factors and CIMP-high
CRC was also evaluated by logistic regression (Table 4 and Table 7). Finally, we used a
multivariate logistic regression model to evaluate the odds ratio of each variable for
CIMP-high tumors. Only a 2-sided p-value of ≤ 0.05 was considered statistically
significant. Only the variables with a p-value less than 0.1 in univariate analysis (Table
3 and Table 4) were put into a multivariate logistic regression model. All the statistical
analyses were performed using SAS statistical software (version 9.4, SAS Institute,
Cary, NC, USA).