Changes of Genetic Loci among Gastric Cancer Patients, Southeastern Iran, 2017
Saeedeh Salari1, Mojgan Noroozi Karimabad2, Masoud Torkzadeh Mahani3, Nahid Askari4, Mohammad Reza Hajizadeh5, Mehdi Mahmoodi6*
1. MSc in Clinical Biochemistry, Dept. of Clinical Biochemistry, Faculty of Medicine, Rafsanjan University of Medical Sciences, Rafsanjan, Iran.
2. Assistant Prof., Molecular Medicine Research Center, Research Institute of Basic Medical Sciences, Rafsanjan University of Medical Sciences, Rafsanjan, Iran.
3. Associate Prof., Dept. of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran.
4. Assistant Prof., Dept. of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran.
5. Associate Prof., Dept. of Clinical Biochemistry, Faculty of Medicine, Rafsanjan University of Medical Sciences, Rafsanjan, Iran; Molecular Medicine Research Center, Research Institute of Basic Medical Sciences, Rafsanjan University of Medical Sciences, Rafsanjan, Iran.
6. Prof., Dept. of Clinical Biochemistry, Afzalipoor Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran; Molecular Medicine Research Center, Research Institute of Basic Medical Sciences, Rafsanjan University of Medical Sciences, Rafsanjan, Iran.
* Corresponding author: Mehdi Mahmoodi; E-mail: mahmoodies@yahoo.com
Abstract
Background: Characterization of genes and precise assessment of the number of copies are crucial for understanding the basis of emergence, progression, and identification of predictive markers of tumor malignancy. This study aimed to investigate the role of the changes in some central genes in gastric cancer.
Materials and Methods: In this experimental study, 30 patients with gastric surgery were selected by random sampling from four hospitals in Kerman to investigate BAX, BCL-2, P53, and MICAL-2 genes in cancerous and healthy tissues. They were then studied using real-time RT-qPCR, PCR- SSCP, and sequencing.
Results: Demographic analysis demonstrated that 66.6% of patients with gastric cancer were men. The age range of men and women was 26-93 and 33-83 years, respectively. In terms of tumor pathology, there was 93.3% adenocarcinoma, 6.6% gastrointestinal stromal tumor (GIST), 16.6% intestinal type, 10% diffuse type, and 73.3% unknown type. The two exons of the p53 gene showed a 2.04 and 3.81 fold increase in expression relative to normal adjacent tissue. Results showed the upregulation of Bcl-2 (1.54%) and MICAL2 (2.23%), while the expression of Bax was downregulated (0.87%). Bcl-2/Bax ratio was not solely correlated with the progression and clinical outcome of gastric cancer.
Conclusion: The data suggest that the changes in BAX, BCL2, P53, and MICAL-2 genes play a key role in gastric cancer.
Keywords: BAX, BCL2, P53, MICAL-2, Sequencing, Gene.
Introduction
Cancer is among the leading reasons for mortality around the globe. It is a long-term process that occurs as a result of abnormal changes in various genes and imbalances in cell cycle regulator mechanisms. Cancer has been demonstrated as the third most common mortality factor in Iran, so that 14% of deaths are related to cancer. Invasion and metastasis are critical determinants of cancer deaths. The genes and molecules participating in these processes must be considered as potential prognostic factors. The incidence of gastric cancer, as a major global health concern, is affected by geographic and ethnic differences all over the world [1]. In recent years, various reports have shown that gastric cancer is the fourth most prevalent cancer in Iran [2, 3]; it is estimated to be the second most common malignancy worldwide. Global estimations have demonstrated that more than 930,000 new gastric cancer cases are diagnosed annually, 700,000 of which are dead [4]. Even though the incidence of gastric cancer is declining, the outcomes of patients with the disease remain disappointing since no sensitive biomarker is available for early prediction of recurrence and chemosensitivity [3, 5]. Infection with Helicobacter pylori represents a strong and established risk factor for gastric cancer; however, it is not sufficient to develop this cancer [6]. Gastric cancer displays transformations in multiple oncogenes, cell cycle regulators, tumor suppressors, and DNA repair genes [7]. In this regard, both Bax and Bcl-2 are vital genes promoting apoptosis, and the sensitivity of cells to apoptotic stimuli is closely related to the ratio of Bcl-2/Bax. Bcl-2 gene, located at 18q21.3, encodes a 25KDa protein located on the nuclear envelope, cytoplasmic side of the mitochondrial outer membrane, and endoplasmic reticulum [8]. Apoptosis is the programmed cell death that plays an essential role in carcinogenesis. The process of apoptosis involves a number of proteins from the Bcl-2 gene family with different functions. Bcl-2 proteins inhibit the mitochondrial pathway of apoptosis through interaction with other members of the Bcl-2 gene family. Apoptotic disorders are related to the development of malignancies such as gastric cancer [8].
On the other hand, p53 tumor antigen is located at 17pl3 and is the most frequently altered gene in human cancers. It is a transcription factor expressed at low levels under normal conditions; its expression is increased upon DNA damage, oncogene activation, nutritional deprivation, and hypoxia [9]. P53 is one of the best-studied genes involved in the formation and/or progression of cancer. It plays a crucial role in tumor suppression, and its mutations can be detected in over half of human cancers [10]. Not only anti-tumor transcriptional activity is lost in mutant p53, but also oncogenic functions are often acquired for promotion of tumor proliferation, invasion, and drug resistance [11]. Although many articles have been published concerning p53 abnormality in patients with gastric cancer, its prognostic impact remains controversial [12]. However, the family of Molecules Interacting with CasL (MICAL) destabilizes F-actin in cytoskeletal dynamics by catalyzing actin oxidation/reduction reactions [13]. This family of multidomain proteins has been conserved from insects to humans, and it is increasingly attracting attention due to participation in several key processes in both health and disease [14]. MICAL-1 has been discovered during screening for CasL-interacting proteins, and a search for proteins that bind to the cytoplasmic domain of plexin receptors has led to the discovery of MICALs. Two more MICAL proteins (MICAL-2 and MICAL-3) have been detected in humans and rodents after identifying MICAL-1 [15]. MICAL-2 is likely to be implicated in prostate cancer progression and could be a novel candidate molecular marker or treatment target in this cancer [13, 16]. Significant overexpression of MICAL2 mRNA has been shown in aggressive, poorly differentiated/undifferentiated, primary human gastric and renal epithelial cancers. Further involvement of MICALs in human cancers has not been explored [13] .Identification of prognostic factors for the diagnosis and determination of optimal therapeutic strategies in patients with gastric cancer is essential [17]. Diagnosis of gastric cancer in the early stages can definitely contribute to better treatment; therefore, the goal of the current study is to investigate the role of BCL-2, BAX, P53, and MICAL-2 genes in the early diagnosis of gastric cancer.
Materials and Methods
This retrospective experimental study was conducted at the laboratory of the Kerman Graduate University of Advanced Technology. Thirty gastric cancer candidates were selected from four hospitals in Kerman (Afzalipour, Fatematalzahra, Payambareazam, Arjmand) in 2017 by random sampling with written permission. The research and its tool were approved by the Research Ethics Committee of Rafsanjan University of Medical Sciences (NO: IR.RUMS.REC.1395.63), and ethical principles were observed during the research. The severity of patients' condition and extensive metastasis were among the reasons for the rejection of samples from which healthy tissue could not be separated from the tumor. Moreover, due to the anesthesia during surgery and lack of standardized nucleic acid stabilization techniques, the tissue could be subjected to hypoxia, changing the expression levels of several genes. Long-term hypoxia reduced the local tissue pH, reducing the nucleic acid yield and quantity, as well as deteriorating the sample. Using simple random sampling and random numbers, 30 samples were chosen for this research. The general formula for random sampling is as follows:
P=1- N-1/N.N-2/N-1….N-n/N-(n-1)
Part of tumor tissue along with adjacent intact tissue (as control) was removed by the surgeon. The samples were kept at -80°C in MEMα to prevent RNA damage. Gastric cancer was diagnosed through appropriate tests, endoscopy, and imaging by specialist physicians. A pathologist was responsible for the diagnosis and separation of tumor tissue from normal tissue. The laboratory mortar was disinfected and autoclaved; then, the tissue samples were cut into small pieces, pulverized in the mortar using liquid nitrogen, and transferred to a 1.5 mL microtube.
DNA and RNA were extracted using Analytic Jena Kit (Jena, Germany) according to the manufacturer's instructions. Finally, 100 μL of elution buffer and 80 μL of RNase-free water were added to DNA and RNA filters, respectively, and incubated for one minute at room temperature, followed by centrifugation at 8,000 g for one minute. The RNAs and DNAs were stored at -80°C and -20°C for the next steps, respectively.
The quantity and quality of DNA and RNA, besides
their absorbance, were measured by a spectrophotometer at 260 and 280 nm wavelengths. The concentration of RNA was calculated using the following formula:
RNA Concentration (μg/mL) = A260 × 40 × dilution factor
The absorbance ratio was calculated at A260/A280 nm. For a pure RNA and DNA sample, this ratio was 1.8.
The concentration of DNA was calculated using the following formula:
DNA Concentration (μg/mL) = A260 × 50 × dilution factor
DNA samples were subsequently stored in a -20°C freezer for later use.
The quality of extracted DNA and RNA was measured using agarose gel electrophoresis [18].
cDNA was synthesized from 1 μg of total RNA using Takara Kit according to the manufacturer's protocol. Three specific primer pairs were used in this study, as listed in Table 1. For each primer, the cDNA concentration and cycling time were optimized. The fragments were amplified in a 20µl reaction volume containing 100 ng cDNA. The selected primers were amplified using Takara Master Kit according to the supplier's instruction. The initial concentration of each sample was normalized against the β-actin reference gene concentration to obtain the expression value.
Table 1. The sequences of primers used for amplifying BAX, BCL-2, P53, MICAL-2, and B-actin genes
Primer |
Primer sequence |
Tm (°C) |
Product Size (bp) |
β- actin |
F:GGACATCCGCAAAGACCTGTA R:ACATCTGCTGGAAGGTGGACA |
57 |
189 |
MICAL-2 |
F:CAACCCGTGTGTGTCTCATC R:GTGGATGCCTGGACAAAGTT |
58 |
209 |
BCL2 |
F: GTGGATGACTGAGTACCTGA R: AGCCAGGAGAAATCAAACAGA |
62 |
119 |
Bax |
F: TTTGCTTCAGGGTTTCATCC R: CAGCTCCATGTTACTGTCCA |
57 |
154 |
P53-4 |
F:AATGGATGATTTGATGCTGTCCC R:CGTGCAAGTCACAGACTTGGC |
57 |
273 |
P53-5 |
F:TTCCTCTTCCTGCAGTACTC R:TCCGTCATGTGCTGTGACTG |
56 |
184 |
P53-6 |
F: GCCATCTACAAGCAGTCACA R: GCCAGACCTAAGAGCAATCA |
57 |
113 |
P53-7 |
F:TTGTCTCCTAGGTTGGCTCT R:CAAGTGGCTCCTGACCTGGA |
58 |
110 |
In this experimental study, real-time-PCR was used to investigate the expression of Bcl-2, Bax, MICAL2, and p53 in normal and tumoral gastric tissues. Moreover, the Bcl-2, Bax, MICAL2, and p53 expression ratio were determined. To investigate the genes, Analytik Jena Kit (Jena, Germany) was used as described above. cDNA was synthesized from RNA by enzymes using a primer hybridizing with RNA. The quantity and purity of the extracted RNA were determined using Cary 60 spectrophotometer, and the OD ratio was measured in A260/A280 nm. Samples with OD260/280 equal to 1.8-2.2 were used for cDNA synthesis. The primers specific to the genes were used in this test. PCR reaction was conducted according to the following program. To amplify the gene fragments, after initial denaturation at 95°C for 2 minutes, PCR reaction was performed in 33 cycles with the thermal program of 95°C for 30 seconds, 58°C for 30 seconds, and 72°C for 15 seconds. The final elongation step was performed for 5 minutes at 72°C.
In order to perform PCR-SSCP, PCR products of different samples were analyzed by polyacrylamide gel electrophoresis. First, the PCR products were incubated at 95°C for 5 minutes for denaturation and were then immediately transferred to an ice-chilled container. Polyacrylamide gel (12%) was used to perform SSCP vertical electrophoresis system. Subsequently, 5 µl of PCR product was added to 5 µl SSCP buffer (formaldehyde 95%, sodium hydroxide 10 mM, bromophenol blue 0.05%, and xylene cyanol 0.05%), and the mixture was loaded into electrophoresis wells. Electrophoresis was performed for 5 hours at 70 V in a 0.6 TBE buffer. The gel was stained with silver nitrate. For this purpose, the gel was placed in solution A (ethanol 10% and acetic acid 0.5%) and was then transferred to solution B (silver nitrate 0.1%) for 10 minutes. It was eventually placed in solution D (Sodium bicarbonate) and was scanned after washing with distilled water.
In order to verify more precisely, based on the size of the target sequence, 2% )w/v( Agarose powder was dissolved in 1X TBE buffer. Later, the gel was kept in ethidium bromide solution for 15 minutes and was then transferred to distilled water for 5 minutes to remove the background stain.
The data were then exported to an Excel worksheet and analyzed with LinRegPCR (v2014.2) program [19].
Results
Statistical analysis of patients' healthcare records (medical notes) showed that the mean age of the patients was 63 years (75±11). The most common age group was 60-90 years, with the predominance of males (66.6%). In the present study of the prevalence of pathologic findings in gastric cancer, most patients had adenocarcinoma. Tumors were classified as intestinal- (16.6%), diffuse (10%) and unknown type (73.4 %) (Table 2).
Table 2. Demographic overview and statistical analysis of patients
|
Frequency of epidemiologic and malignancy indicators |
Number |
Percentage |
Age |
60≤ |
17 |
56.6 |
60> |
13 |
43.3 |
|
Gender |
Male |
20 |
66.6 |
Female |
10 |
33.3 |
|
Tumor type pathology |
Adenocarcinoma |
27 |
93.3 |
Lymphoma |
0 |
0 |
|
GIST |
3 |
6.6 |
|
Pathology of gastric carcinoma |
Intestinal |
5 |
16.6 |
Diffuse |
3 |
10 |
|
Unknown |
22 |
73.3 |
|
Tumor differentiation grade |
Good differentiation |
2 |
6.6 |
Intermediate differentiation |
8 |
26.6 |
|
Poor differentiation |
20 |
66.6 |
After extracting DNA and RNA, their purity and quality were read in a Nanodrop device using an RNX-plusTM kit (CinnaGen), and an OD ratio of A260/A280 for RNA was obtained, which is approximately equal to 2 in optimal conditions. Moreover, the extracted DNA and RNA were electrophoresed on agarose gel (Fig. 1).