Molecular pathology of colorectal cancer: The Saudi situation in perspective

Abdulaziz Alfahed

doi:10.15537/smj.2023.44.9.20230257

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Table 1

- Molecular pathology of colorectal cancer syndromes from Saudi patients.

Syndromes	Germline alterations	Molecular methodology	Sample size	References
Lynch syndrome	PMS2 c.1376C>G, p.S459X, MLH1 c.1652A>C, p. N551T MSH2 c.2262-2267 delTTCTAC, p.T756-Y757 del MSH2 c.1226_1227delAG MSH2 c.1964.delT, p. V655fs MSH2 c.289C>T, Q97* MSH6 c.3475insT, p. Y1159fs MSH6 c.3475insT	MMR protein by IHC, MSI, and BRAF mutation testing and deep sequencing	2.2% of all CRC (N=1207)	19,20
Lynch syndrome	MSH2 c.737A>T, p.K246I MSH2 c. 2262_2267del, p.S755_T756del MSH2 c.367-? __1276+? Del MSH2 c.2089T>C, p.C697R MSH2 c. 2038C>T, p.R680* MLH1 c.62C>T, p.A21V MLH1 c.1961C>T, p.P654L MLH1 c.677G>A, p.R226Q MLH1 c.454-?_545+?del	MMR protein by IHC, MSI, BRAF mutation testing, MLPA, deep sequencing, and Sanger sequencing	7.2% of all CRC (N=284)	21
Lynch syndrome	Deletion of chromosomal regions: 2p21-2p16.3 (MSH2, MSH6, and EPCAM) 3p23-3p14.2 (MLH1) 7p22.1 (PMS2) 1p34.1-1p33 (MUTYH)	Whole genome comparative genomic hybridization array	N=12 (LS patients)	24
FAP syndrome	PMS2 c.1376C>G, p.S459X	WES	One case report	19

FAP: familial adenomatous polyposis, MMR: mismatch repair, IHC: immunohistochemistry, MSI: microsatellite instability, BRAF: B-Raf, MLPA: multiplex ligation probe amplification, WES: whole-exome sequencing, CRC: colorectal cancer, LS: Lynch syndrome

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Table 2

- Genetic risks for colorectal cancer in Saudi patients.

Genetic loci	Study approach	Number of CRC cases	Molecular methodologies	Risk patterns	References
ABCC1 C218T	Case-control	N=51, 65 controls	PCR-RFLP and DNA sequencing (Sanger)	Increased CRC risk, OR=3.4	40
ADIPOQ G276T	Case-control	N=60, 60 controls	PCR-RFLP	Increased CRC risk, OR=2.64	41
CYP1A1wt/*2A	Case-control	N=92, 79 controls	PCR-RFLP	Increased CRC risk, OR=3.65	42
GSTM1	Case-control	N=80, 78 controls	Diplex PCR	Increased CRC risk, OR=3.7	43
TP53 rs1042522	Case-control	N=80, 78 controls	TaqMan real-time PCR assays	Increased CRC risk, OR=1.6	43
KIR 2DS1, 2DS2, 2DS3, 2DS5, and 3DS1	Case-control	N=70, 70 controls	PCR	Increased CRC risk, OR=8.6-fold, 3-fold, 2.5-fold, 4.5-fold, and 16.25-fold	44
IL17A rs2275913: GA and AA genotypes	Case-control	N=117, 100 controls	TaqMan allelic discrimination assay (PCR)	Increased CRC risk, OR=2-fold and 2.8-fold	45
NOTCH3 rs1043994: G>A	Case-control	N=134, 139 controls	TaqMan allelic discrimination assay (PCR)	Increased CRC risk in males, OR=1.971	46
PARP1 K933N and K945N ‎	Case-control	N=50, 50 controls	PCR and Sanger sequencing	Increased CRC risk OR=3.1429 for K933N G>T heterozygote; OR=2.5714 for K945N G>T heterozygote	47
PRNCR1 rs1456315: CC genotype	Case-control	N=144, 130 controls	TaqMan assays	Increased CRC risk, OR=2.09	48
RETN rs1862513 and rs375367	Case-control	N=60, 60 controls	PCR-RFLP	Increased CRC risk, OR=2.48 (rs1862513); OR=6.5 (rs375367)	49
TDG rs4135113	Case-control	N=100, 192 controls	TaqMan genotyping	Increased CRC risk, OR>3.6; OR=5 in those >57 years	50
TLR9 rs352139	Case-control	N=115, 102 controls	TaqMan allelic discrimination assay (PCR)	Increased CRC risk for rectal cancers, OR=3.552 and 1.809 for GG genotype and G allele	51
TNFA rs361525 (G238A)	Case-control	N=100, 100 controls	TaqMan allelic discrimination assay	Increased CRC risk, OR=14.663 for AA genotype and 7.647 for the A allele	52
TSLP rs10043985	Case-control	N=112, 108 controls	TaqMan genotyping assay	Increased CRC risk, OR=16.52 for AC genotype and 10.837 for the C allele	53
VDR1 ApaI rs797232	Case-control	N=100, 100 controls	PCR amplification, followed by Sanger sequencing	Increased CRC risk, OR=1.778 in patients >57 years (rs797232 and C allele)	54
VDR1 TaqI rs731236	Case-control	N=132, 124 controls	PCR-RFLP	Increased CRC risk, OR=6.18	55
XRCC1 A399G	Case-control	N=100, 100 controls	PCR-RFLP and PCR-CTPP	Increased CRC risk, OR=2.1	56
ABCB1 G2677T	Case-control	N=62, 100 controls	PCR-RFLP	Reduced CRC risk, OR=0.004 for heterozygotes GT and 0.005 homozygotes TT	57
ADIPOQ T45G	Case-control	N=60, 60 controls	PCR-RFLP	Reduced CRC risk, OR=0.41 for the G allele	41
CTNNB1 rs4135385	Case-control	N=122, 110 controls	TaqMan assays	Reduced CRC risk, OR=0.092 for GG genotype	58
LRP6 rs2284396	Case-control	N=122, 110 controls	TaqMan assays	Reduced CRC risk, OR=0.250 for the CC genotype in cases >57 years; OR=0.561 for the C allele	58
SFRP3 rs7775	Case-control	N=122, 110 controls	TaqMan assays	Reduced CRC risk, OR=0.397 for the Gly allele in female gender	58
CYP19A1 rs4774585 rs4775936	Case-control	N=100, 100 controls	TaqMan genotyping by real-time PCR	Reduced CRC risk, OR=0.28 for rs4774585 AA genotype in the male gender; OR=0.37 for rs4775936 CT genotype in the female	59
IL7R rs1053496	Case-control	N=112, 108 controls	TaqMan genotyping assay	Reduced CRC risk, OR=0.529, 0.467 and 0.644 for the CT and TT genotypes, and the T allele	53
PARP1 rs8679	Case-control	N=183, 190 controls	TaqMan assay	Reduced CRC risk, OR=0.566 for the TC genotype and 0.695 for the C allele	60
TDG rs1866074 rs3751209	Case-control	N=100, 192 controls	TaqMan genotyping	Reduced CRC risk, OR=0.501 for rs1866074 GG genotype; OR=0.407 for rs3751209 GA genotype in the male gender	50
TLR4 rs10759931 rs2770150	Case-control	N=115, 102 controls	TaqMan allelic discrimination assay	Reduced CRC risk, OR=0.052, 0.018 and 0.085 for rs10759931 GA and AA genotypes, and A allele, respectively; OR=0.074, 0.194, 0.188 for rs2770150 TC and CC genotypes, and C allele only in the female gender	61
TLR9 rs187084 rs352144	Case-control	N=115, 102 controls	TaqMan allelic discrimination assay (PCR)	Reduced CRC risk, OR=0.527 for rs187084 T allele in the female gender; OR=0.067 for rs352144 AC genotype for rectal tumours	51
VDR1 BsmI rs1544410	Case-control	N=100, 100 controls	PCR amplification, followed by Sanger sequencing	OR=0.217 for rs1544410 AA genotype and 0.442 for A allele in the female gender	54

PCR-RFLP: polymerase chain reaction-restriction fragment length polymorphism, CRC: colorectal cancer, OR: odds ratio

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Table 3

- Somatic mutations in colorectal cancer from Saudi patients.

Genes	Mutation rates (mutation type)	Sample sizes	Molecular methodologies	References
KRAS	56.0% (point)	150	PCR followed by amplicon hybridization	68
	28.6% (point)	755	PCR and DNA sequencing	69
	30.1% (point)	498	PCR and DNA sequencing	70
	50.0% (point)	194	Biocartis Idylla^Tm	71
	45.2% (point)	93	NGS	72
	42.2% (point)	83	PCR followed by amplicon hybridization	73
	49.6% (point)	248	Biocartis Idylla^Tm	74
	35.0% (point)	99	Ion PGM sequencing	75
	32.5% (point)	80	Sanger sequencing	76
	42.85% (point)	56	HRM analysis, Sanger sequencing, and shifted termination assays	77
	42.0% (point)	300	LCD-array	78
	43.0% (point)	51	Ion AmpliSeq NGS Panel	79
	25.0% (point)	99	Ion AmpliSeq™	80
NRAS	2.2% (point)	93	NGS	72
NRAS	2.0% (point)	248	Biocartis Idylla^Tm	74
BRAF	2.5% (point)	757	PCR and DNA sequencing	69
	2.4% (point)	498	PCR and DNA sequencing	70
	2.2% (point)	93	NGS	72
	0.4% (point)	248	Biocartis Idylla^Tm	74
PIK3CA	19.0% (point)	99	Ion PGM Sequencing	75
PIK3CA	12.2% (point)‎	418	Sanger sequencing	81
HER2 (ERBB2)	0.0% (gene amplification)	114	FISH	82
HER2 (ERBB2)	51.0% (point)‎	99	Ion AmpliSeq™	80
CCND1	1.9% (gene amplification)	114	FISH	82
EGFR	11.0% (point)	99	Ion PGM Sequencing	75
	1.1% (gene amplification)	114	FISH	82
	40.0% (point)	99	Ion AmpliSeq™	80
C-MYC	9.0% (gene amplification)	114	FISH	82
MSI	11.2%	741	Microsatellite analysis by multiplex fluorescent PCR	69
	10.9%	494	Microsatellite analysis by multiplex fluorescent PCR	70
	20.2%	388	Microsatellite analysis by multiplex fluorescent PCR	81
	9.7%	992	Microsatellite analysis by multiplex fluorescent PCR	83
	11.6%	284	Pentaplex MSI analysis system	84
	11.3%‎	807	Microsatellite analysis by multiplex fluorescent PCR and immunohistochemistry assessment	20
TP53	65.0% (point)	99	Ion PGM sequencing	75
	33.7% (point)	386	Sanger sequencing	81
	19.0% (point)	99	AmpliSeq comprehensive	80
APC	36.0% (point)	99	Ion PGM sequencing	75
APC	66.0% (point)	99	AmpliSeq comprehensive cancer panel	80
SMAD4	11.0% (point)	99	Ion PGM sequencing	75
	3.0% (point)‎	99	AmpliSeq comprehensive cancer panel	80
	13.6% (point)‎	426	High depth capture sequencing	83
	60.8% (SMAD4 gene and 18q deletion)	991	FISH	83
PTEN	13.0% (point)	99	Ion PGM sequencing	75
	3.0% (point)	99	AmpliSeq comprehensive cancer panel	80
	66.1% (point)	386	Sanger sequencing	81
CIMP	CIMP-H=4.8%; CIMP-L=44.6%; CIMP-negative=50.6%	500	Real-time PCR (MethyLight)	70

MSI: microsatellite instability, CIMP: CpG island methylator phenotype, CIMP-H: CpG island methylator phenotype-high, CIMP-L: CpG island methylator phenotype-low, PCR: polymerase chain reaction, PGM: personal genome machine, FISH: fluorescence in situ hybridisation, HRM: high resolution melt, LCD: liquid-crystal display, NGS: next-generation sequencing