Study design and participants
One hundred and five patients with EC and 105 healthy controls were recruited in this hospital-based case–control study, approved by the Khon Kaen University Ethics Committee for Human Research (HE621269).
The control group patients were admitted with esophagitis at the same time as the cancer cases. The cases and controls were recruited from Srinagaring Hospital in Khon Kaen province, Northeast Thailand, from 2007 to 2017. Data collection was conducted by trained nurses. The EC cases comprised new patients whose diagnosis was clinically and histologically confirmed according to International Classification of Diseases for Oncology, 3rd Edition (ICD-O-3) codes: C15.3, C15.4, C15.5, C15.8, C15.9 and C16.0. The histological diagnosis was reviewed in each case and confirmed by two pathologists, and the medical reports were obtained from the pathology department.
The control subjects were healthy individuals, confirmed upon physical examination, who underwent clinical and biochemical analysis during the same period that the cases group were recruited. Eligible controls included individuals without a history of gastric or esophageal malignancy. The subjects were randomly sampled from patients undergoing routine endoscopy for investigation of presumed nonmalignant conditions, such as GERD. A criterion was that their esophageal biopsies had to be macroscopically normal in appearance. The participants provided written informed consent to participate in the current study.
Data on the subjects were obtained using an interviewer-based structured questionnaire. Prior to data collection, trained staff served as interviewers to ensure the validity of the questionnaire questions. The demographic information sought included age, gender, height, weight, smoking status, alcohol consumption, a family history of cancer, oral hygiene practices and a history of GERD. Data on cigarette smoking included the age of smoking started, the number of cigarettes smoked per day and smoking duration. A smoker was defined as a current smoker who smoked at least one cigarette per day, having done so for at least six months. Alcohol consumption was divided into two group (drinkers and non-drinkers). Drinking status was defined as drinking alcohol at least once a day for at least six months; non-drinkers were those who consumed alcohol less than once a month. Detailed information was obtained on the participants’ oral hygiene practices, for example, the daily frequency with which they brushed their teeth (never, less than once a day, twice or more per day), the type of instrument used to clean their teeth, the regularity of dental visits (never, annually and every 2–5 years) and a previous history of gingivitis or periodontal disease.
Tissue samples
Formalin-fixed paraffin-embedded (FFPE) samples (N = 210; n = 105 EC samples [case group] and n = 105 normal tissue samples [control group]) were collected retrospectively between 2007 to 2017 and retrieved from paraffin blocks stored at the Department of Pathology, Faculty of Medicine, Khon Kean University. Esophageal squamous cell carcinoma (ESCC) and Esophageal adenocarcinoma samples were categorized in the case group, and normal esophageal tissue samples were assigned to the control group. The samples were initially evaluated by a specialist; thereafter, the diagnoses were confirmed using electronic gastroscopy, a histopathology report and ICD-O-3 guidance.
Laboratory methods
DNA extraction and quality control
DNA was extracted from the FFPE tissue. The FFPE esophageal tissue was cut into 10 µM sections placed in a 1.5 microcentifuge tube. Eight sections from each sample were used for DNA extraction. Prior to sectioning, the microtomes and accessories were cleaned using 70% ethanol alcohol. The DNA of the FFPE tissue samples was extracted using a commercially available system, DNeasy® Blood & Tissue Kits (Qiagen, Hilden, Germany), according to the manufacturer’s instructions. Briefly, eight sections (10 µM each) from each FFPE tissue specimen were deparaffinised in xylene and 95% ethanol. The deparaffinised tissue was washed twice with 95% ethanol; 1,000 μl of ethanol was added and vortexed for 30 seconds and then centrifuged at 13,000 rpm for five minutes. The tissue pellets were then washed with distilled water and air dried. The recommended protocols for DNA FFPE extraction were followed (Qiagen, DNA FFPE Tissue®, Germany). The yields and quality of the DNA isolated during the process were determined using a NanoDrop® ND-1000 Spectrophotometer (Thermo Scientific, Wilmington, USA). The housekeeping gene (β-actin) served as an endogenous control to guarantee the DNA quality and was detected using a specific primer (forward 5’- TGTCACAGTGCAAGCTCACTCAGT-3’, reverse 5’- TCCTGAGGAGAAGTCTGCCGTT-3′), following the protocols described elsewhere [35]. The integrity of the extracted DNA samples was confirmed by amplifying the housekeeping gene (β-actin) using SYBR Green-based real-time polymerase chain reaction (real-time PCR). The DNA samples were stored at -20 °C for further analysis.
Campylobacter species detection using a TaqMan® real-time PCR assay
To detect Campylobacter infection, a TaqMan® real-time PCR detection system, which utilizes fluorogenic-labelled probes, was used to determine the infection agent count [36]. Specific TaqMan® PCR primers and fluorescently labelled probes (Table 1) were designed using the Oligoware® 1.0 software program (Integrated DNA Technology, Coralville, USA). Thereafter, theoretical testing was conducted on the candidate primers and probes, and sequence comparisons were made using the BLAST database (National Institutes of Health, USA). For each infectious agent tested, the TaqMan® PCR assay was performed (a final volume of 20 μl for the PCR reaction). Each reaction comprised 1 × THUNDERBIRD™ qPCR Mix (Toyobo Co. Ltd., Japan), 10 µl of TaqMan® qPCR Mix, 0.3 µM of each forward and reverse primer, 0.2 µM of TaqMan® probe and 50 ng of DNA template. The amplification, data acquisition and Campylobacter genus DNA analysis was carried out using an Applied Biosystems® 7500 flats system.
PCR amplification comprised an initial denaturation cycle at 95 °C for five minutes, followed by 40 amplification cycles at 95 °C for 30 seconds, annealing at 55 °C for 22 seconds and final extension at 72 °C for 30 seconds. The Campylobacter spp. cycling conditions were as follows: initial denaturation with five minutes at 95 °C, followed by 40 amplification cycles at 95 °C for 30 seconds, a specific Tm set for each primer for 30 seconds and final extension at 72 °C for 30 seconds. DNA was extracted from three strains following sequencing of the 16S rRNA genes and used as the positive control as in Table1, and molecular distilled water was used as the negative control. Both were utilized in each PCR assay run. The samples and controls were tested in duplicate, and the considered positive were replicated following amplification within a cycle of < 36.
Statistical analysis
The demographic characteristics of the subjects were summarized using descriptive statistics. The categorical data were expressed using frequencies and percentages, and the continuous data, such as the age of the subjects, were depicted by mean ± standard deviation (SD), median, and minimum and maximum range. Bivariate analysis was performed using simple logistic regression to determine the association between the independent factors and EC, without controlling for confounding variables. The crude odds ratio (OR crude) and the 95% confidence interval (95% CI) were also calculated. Unconditional multivariable logistic regression was used to compute the adjusted ORs (ORadj) and 95% CIs for the association between EC risk factors and EC, while controlling for the effects of confounding variables. The test statistics were two-sided, and a p-value less than 0.05 was considered statistically significant. The statistical analysis was performed using Stata® software (version 13.0).