2.1 Ethics Statement and Human Participants
The current research had the approval of the Deanship of Scientific Research for Princess Nourah Bint Abdulrahman University. This study was approved by national regulation committee of ethics, KACST, KSA (study number H-01-R059, IRB LOG number 20-0287). Additionally, the written acquainted permissions have been obtained from the participating patients prior to obtaining their samples
2.2 Case Selection and Samples Collection
Theis research data was made up of 24 consanguineous cases of affected carriers and patients from a single Saudi family (for four generations) from Riyadh, Saudi Arabia. From 24 relatives, three samples of biopsies were obtained from relatives affected by malignant cancer of the colon in 2020 (August) at the King Fahad Medical City (KFMC) in Riyadh, Saudi Arabia.
The benchmark demographic profiles entailed all the participating consanguineous cases that is summarised in (Table 1). TNM’s classifications of malignant cancer of the colon for the participating consanguineous cases affected patients showing malignant cancer of the colon are l shown in (Table 2).
Table 1. Benchmark demographic profiles showing clinical characteristics for the participating consanguineous cases in four generations together with their consanguineous cases mutated couples
Cases #
|
Age at diagnosis (years)
|
Gender
|
Family history with other types of cancer
|
Diagnosed with colon cancer
|
BRCA1 & BRCA2 mutations
|
Smoking history
|
Chronic colitis history
|
Obesity
(BMI ≥ 25 kg)
|
1
|
79
|
M
|
unknown
|
YES
|
YES
|
-
|
-
|
-
|
2
|
76
|
F
|
-
|
-
|
YES
|
-
|
-
|
YES
|
3
|
59
|
M
|
YES – breast
|
-
|
YES
|
YES
|
YES
|
-
|
4
|
55
|
F
|
YES – pancreatic & breast
|
-
|
YES
|
-
|
-
|
YES
|
5
|
55
|
M
|
YES – breast
|
-
|
YES
|
-
|
-
|
-
|
6
|
53
|
F
|
YES – breast
|
-
|
YES
|
-
|
YES
|
YES
|
7
|
51
|
M
|
YES – breast
|
-
|
YES
|
YES
|
YES
|
-
|
8
|
48
|
F
|
YES – breast
|
-
|
YES
|
-
|
-
|
YES
|
9
|
46
|
F
|
YES – breast
|
-
|
YES
|
-
|
-
|
-
|
10
|
39
|
M
|
YES – breast
|
-
|
YES
|
-
|
YES
|
-
|
11
|
38
|
F
|
YES – pancreatic & breast
|
-
|
YES
|
-
|
YES
|
-
|
12
|
36
|
F
|
YES – breast
|
-
|
YES
|
YES
|
-
|
YES
|
13
|
34
|
F
|
YES – breast
|
YES
|
YES
|
-
|
YES
|
YES
|
14
|
31
|
M
|
YES – breast
|
-
|
YES
|
-
|
-
|
-
|
15
|
30
|
M
|
YES – breast
|
-
|
YES
|
YES
|
-
|
YES
|
16
|
28
|
F
|
YES – breast
|
-
|
YES
|
-
|
-
|
-
|
17
|
24
|
F
|
YES – breast
|
-
|
YES
|
-
|
-
|
-
|
18
|
17
|
F
|
YES – breast
|
YES
|
YES
|
-
|
YES
|
YES
|
19
|
14
|
M
|
YES – breast
|
-
|
YES
|
-
|
-
|
-
|
20
|
12
|
F
|
YES – breast
|
-
|
-
|
-
|
-
|
-
|
21
|
10
|
F
|
YES – breast
|
-
|
YES
|
-
|
-
|
-
|
22
|
7
|
M
|
YES – breast
|
-
|
YES
|
-
|
-
|
-
|
23
|
6
|
F
|
YES – breast
|
-
|
-
|
-
|
-
|
-
|
24
|
6
|
F
|
YES – breast
|
-
|
-
|
-
|
-
|
-
|
Total
|
22/24
|
3/24
|
21/24
|
4/24
|
7/24
|
8/24
|
Table 2. Pathological characteristics (TNM classifications) for the participating consanguineous cases having malignant cancer of the colon.
Stage (TNM Classification)
|
Number of Patients (%)
|
T1 - Tumor affects the submucosa (1-2 cm)
|
2
|
T2 - Tumor affects the muscularis propria (5 cm)
|
1
|
Total
|
3
|
DNA Extraction
Samples of blood were obtained from all the consanguineous cases affected carriers and patients from a single Saudi family (for four generations). Then, DNA was collected using the Qiagen DNA isolation kit (Cat No./ID: 69506, Quigen, Hilden, Germany) using the instructions of the manufacturer. The sample concentration and quality DNA ratio were assessed by use of the NanoDrop Spectrophotometer system (Thermo Scientific, USA).
Targeted Capture Sequencing of BRCA2 /BRCA1 Mutations
Exon coding sequences for the BRCA2 BRCA1 genes were put under heteroduplex analysis, according to the description by [16] or the single-stranded conformation analysis, according to the description by [17].
PCR and Sanger Sequencing for Detection of BRCA2/ BRAC1 Mutations
The whole coding sections of BRCA2 and BRCA1 used the conventional Sanger sequencing technique. The primer 3 program was used for designing the primers of all the coding exons for BRCA2 and BRCA1 genes. The primers’ sequences for BRCA2 and BRCA1 are shown in Table 3 b& a respectively. The nucleoFast ® 96 PCR Clean-up kit purified PCR products, according to the instructions of the manufacturer.
The reactions of sequencing were done utilising the BigDye ® Terminator v1.1 Cycle Sequencing kit in every PCR product (purified). The sequencing reaction products were purified utilising the MontageTM SEQ96 Sequencing Reaction kit, that followed by some electrophoresis by Applied Biosystems 3130 Genetic Analyzer, which is similar to the previous study [18].
Table 3. BRCA2 and BRCA1 PCR primers
a) BRCA1 Primers Sequence
Exon 2
|
Forward
|
5'-GAAGTTGTCATTTTATAAACCTTT-3'
|
315
bp
|
Reverse
|
5'-TGTCTTTTCTTCCCTAGTATGT-3'
|
Exon 5
|
Forward
|
5'-GCTCTTCGCGTTGAAGAAGT-3'
|
400
bp
|
Revers e
|
5'-GAAGTCTTTTGGCACGGTTT-3'
|
Exon 8
|
Forward
|
5'-CAGCTTGACACAGGTTTGGA-3'
|
499
bp
|
Reverse
|
5'-TTTCTGGATGCCTCTCAGCT-3'
|
Exon 11
|
Forward
|
5'-GAGGACAAAGCAGCGGATAC-3'
|
359
bp
|
Reverse
|
5'- GCTGTAATGAGCTGGCATGA-3'
|
Exon 18
|
Forward
|
5'- GGGAGAAGCCAGAATTGACA-3'
|
354
bp
|
Reverse
|
5'- CTCGCTTTGGACCTTGGTG -3'
|
Exon23
|
Forward
|
5'- TTCAGGGGGCTAGAAATCTG-3'
|
289
bp
|
Reverse
|
5'- AAGCTCATTCTTGGGGTCCT -3'
|
Exon24
|
Forward
|
5'- TTCAGGGGGCTAGAAATCTG-3'
|
289
bp
|
Reverse
|
5'- GGGGTATCAGGTAGGTGTCC-3'
|
b) BRCA2 Primers Sequence
Exon 2
|
Forward
|
5'- AGCGTGAGGGGACAGATTTG-3'
|
519
bp
|
|
Reverse
|
5'-GTGGACAGGAAACATCATCTGC -3'
|
Exon 9
|
Forward
|
5'- AGGAGCTGAGGTGGATCCTG -3'
|
980
bp
|
|
Reverse
|
5'- TCAGAATTGTCCCAAAAGAGCT -3'
|
Exon 9
|
Forward
|
5'- GTTCAGCCCAGTTTGAAGCA -3'
|
980
bp
|
|
Reverse
|
5'- TGACACTTGGGTTGCTTGTT -3'
|
Exon 14
|
Forward
|
5'- TGTCCCGAAAATGAGGAAATGG -3'
|
925
bp
|
|
Reverse
|
5'- TGTGAAACTGAAAAGACTCTGCA -3'
|
Exon 18
|
Forward
|
5'- GGTGGATGGCTCATACCCTC -3'
|
809
bp
|
|
Reverse
|
5'-TTTGCTGCTTCCTTTTCTTCC-3'
|
Exon 23
|
Forward
|
5'- GAAGAATGCAGCAGACCCAG -3'
|
751
bp
|
|
Reverse
|
5'- TGTCTCTTGAAAGTGGCCCT-3'
|
Quantitative Genome Analysis
Sequence data was confirmed visually using the snap gene viewer (SGV). BRCA2 (accession number: NP_000050.2) and GenBank BRCA1 human sequences(accession number: NP_009225.1) were referenced to the NCBI Reference Sequences Database.
Pedigree Analysis
History of colon cancer including particular factors: carriers of BRCA2 and BRCA1 gene mutations, age-of-onset, tumors type, endogamy, other history of cancer, cause and date of death was determined for all the descendants of traceable ancestors for the patients having colon cancer. Cancer incidence and pedigree data were registered on a database (computerized). The traceable consanguineous cases were the ones living between 2019- 2020.
Tissue and Histological Preparation
Tissue specimens consisted of small biopsies i.e., 7-10 mm in diameter and were obtained from consanguineous cases affected patients having malignant cancer of the colon. Later, tissue specimens underwent transfer to 10% formalin fixative (buffered). After processing of tissue in an automated tissue’s processor applying a schedule for 24 hours, blocks of paraffin were sectioned and made to attain sections of 3-5 µm for the conventional histopathology. Then, conventional histopathology applied the Hematoxylin and Eosin (H&E) technique, as described [19].
Immunohistochemical Stating for BRCA1&2
In accordance with the major aim of BRCA1&2 IHC expression of screening and confirming inherited germline’s mutations in order to examine BRCA1&2 deficiency linked to a number of biological mechanisms.
Immunohistochemical researches were done in samples obtained from all the consanguineous cases subjects having colon cancer got from the blocks embedded with paraffin. Sections of 5 µm obtained from paraffin-embedded wax blocks then were put in slides (saline-glass) and later air-dried for a night at 37°C, deparaffinised in xylene, followed by rehydration in some graded alcohol (70 and 100%). The slides were then incubated in 3% methanol/ H2O2 for 10 minutes and washed by phosphate-buffered saline (PBS). Primary antibodies in the study for : anti-BRCA1 (MS110, mouse monoclonal, 1:200, Abcam, Cambridge, UK), anti-BRCA2 (MAB2476, mouse monoclonal, 1:500, R&D Systems, Inc. Minneapolis, MN, USA) were utilised at a diluted ration of 1:10, and then recorded as negative (absent or greatly reduced) in case the brown-like nuclear stain indicated <20% whereas nuclear staining of >20% was regarded as positive (American society of clinical oncology/college of American pathologist clinical practice guideline update 2013). Later, the sections were subjected to incubation for half a day in the primary antibodies BRCA2 and BRCA1 at 4°C washed using PBS. Consequently, a light microscope was used to examine for any immunostained sections.
Analysis of Statistics
The analytical examinations applied the SigmaStat programming adaptation 3.5 (Systat Software, San Jose, CA, USA). Later, the quantitative outcomes’ results were expressed in terms of, standard deviations and mean. P values < 0.05, were regarded as statically significant.