KRAS, BRAF, PIK3CA mutation frequency of radical prostatectomy samples and review of the literature

Figures & data

Figure 1. Selection of cases.

Table 1. Stage and TNM status of patients according to the groups.

	GS-L (Gleason score ≤ 6) n	GS-H (Gleason score ≥ 9) n
T
pT2	12 (100.0%)	5 (41.7%)
pT3a	0	2 (16.7%)
pT3b	0	5 (41.7%)
N
N0	11 (91.7%)	10 (83.3%)
N1	1 (8.3)	2 (16.7%)
M
M0	11 (91.7)	11 (91.7%)
M1	1 (8.3)	1 (8.3%)
Stage
I	10 (83.3)	0
IIA	1 (8.3)	0
IIIC	0	9 (75.0%)
IVA	0	2 (16.7%)
IVB	1 (8.3)	1 (8.3%)

Figure 2. (A) Weak staining with EGFR in neoplastic glands (EGFRx200). (B) EGFR strong staining (EGFRx200). (C) Intense and strong staining with P16 in tumoral glands, negativity in the benign gland adjacent (P16 × 200). (D) No staining in neoplastic glands with HER2 (HER2 × 400).

Table 2. KRAS, BRAF and PIK3CA mutation and HER2, EGFR, and p16 expression status of cases according to groups.

	GS-L	GS-H	Total	p*
	n	n	n
KRAS
mutation	3 (25%)	0	3 (12.5%)	.217^&
BRAF
mutation	0	0	0	–
PIK3CA
mutation	0	0	0	–
HER2
positivity	0	0	0	–
EGFR
weak	9 (75%)	6 (50%)	15 (62.5%)
moderate	2 (16.7%)	5 (41.7%)	7 (29.2%)	.271^$
strong	0	1 (8,3%)	1 (4.2%)
P16
weak	3 (25%)	6 (50%)	9 (37.5%)
moderate	6 (50%)	4 (33.3%)	10 (41.7%)	.350^$
strong	0	1 (8,3%)	1 (4.2%)

*Exact p value, ^&Fisher Exact test, ^$Fisher Freeman Halton test.

Table 3. KRAS, BRAF and PIK3CA mutations in human PCa tissues in the literature.

		KRAS	BRAF	PIK3CA	n	+ codon	method
1	Carter 90	0%	–	–	24	–	PCR/Oligodeoxynucleotide hybridization
2	Capella 91	0%	–	–	10	–	PCR/Oligonucleotide hybridization
3	Gumerlock 91	0%	–	–	19	–	PCR/Oligonucleotide hybridization
4	Konishi 92	%26	–	–	23	KRAS 12	PCR/Oligonucleotide hybridization
5	Moul 92	0%	–	–	24	-	PCR/Oligonucleotide hybridization
6	Anwar 92	2.6%	–	–	75	KRAS 12, 61	PCR/Oligonucleotide hybridization
7	Pergolizzi 93	6.2%	–	–	16	KRAS 12	PCR/Oligonucleotide hybridization
8	Watanabe 94	14.2% Japanese 5% Hawaiian Japanese 0% Colombian 0% US white 0% US black	–	–	21 Japanese 20 Hawaiian Japanese 10 Colombian 15 US white 15 US black	KRAS 12, 61	PCR/Oligonucleotide hybridization
9	Suzuki 94	11%	–	–	18	KRAS 12, 61	Direct sequencing PCR/ SSCP (Single Strand Conformation Polymorphism)
10	Konishi 95	22%	–	–	9	KRAS 13, 61 1 case combined 13-61	Direct sequencing PCR/ SSCP
11	Moyret-Lalle 95	0%	–	–	27	–	Direct sequencing PCR/SSCP
12	Konishi 97	12.9% Japanese 3.2% American	–	–	70 Japanese 30 American	KRAS 12	Direct sequencing PCR/SSCP
13	Shiraishi 98	16%	–	–	81	KRAS 12	PCR/SSCP MASA (Mutant Allele-Specific Amplification)
14	Cho 2006	7.3%	10.2%	–	206	KRAS 12,13 BRAF V600E, V600M, V600A	PCR-RFLP (Restriction Fragment Length Polymorphism) ve direct sequencing
15	MacConaill 2009	0%	0%	2.1%	95	PIK3CA H1047R G1049R	PCR/Sanger sequencing Mass spectrometry genotyping
16	Shen 2010	9.1%	0%	–	121	KRAS 12,13	ME (mutation enriched)-PCR couplet sequencing
17	Taylor 2010	1.2%	0 %	1.2%	156	KRAS 12 PIK3CA E545K, H1047R	PCR/ Mass spectrometry (iPLEX Sequenom)
18	Choi 2010	29.1%	6.8%	–	103	KRAS 12 BRAF V600E	PCR/Sequencing
19	Agell 2011	0%	0%	0%	102	–	PCR/Direct sequencing
20	Ren 2012	3.1%	0%	–	96	KRAS 12	PCR/ Taqman quantitative method Sanger sequencing
21	Sha 2012	8.91% Pyrosequencing 3.96% Sanger sequencing	–	–	101	KRAS 12,13	Pyrosequencing Sanger sequencing
22	Silan 2012	40%	–	–	30	KRAS 12, 13 9 case combined 12-13	PCR/StripAssay automatic reverse hybridization
23	Grasso 2012	̴1.6%	–	–	59	^#	Exome sequencing
24	Barnett 2014	0%	0%	4.5%	40	PIK3CA Q546P, H1047R	Sequenom MassArray mass spectrometry and Sanger sequencing
25	Fu 2014	2.3 %	–	–	88	KRAS 12, 13	PCR/Sanger sequencing
26	Salmaninejad 2015	5.7%	0%	–	35	KRAS 12, 13	PCR/Sanger sequencing
27	Vural 2018	8,8%	–	–	45	KRAS Exon 2, exon 3*	PCR/High resolution DNA melting analysis
28	Martinez-Gonzalez 2018	28.3%	5%	3.3%	60	KRAS 12, 13 BRAF V600E PIK3CA Q546P, H1047Y	ARMS (Amplification Refractory Mutation System) PCR/Custom qBiomarker Somatic Mutation PCR Arrays Probe based analysis
29	Jaratlerdrisi 2018	0.7%	–	0%	15	^#	Whole genome sequencing
30	Ikeda 2019	2.8%	0%	10.4%	67	^#	NGS (Next Generation Sequencing)
31	Toomey 2020	0%	0%	4.8%	83	^#	PCR/Mass spectrometry based single nucleotide polymorphism genotyping technology (Agena MassArray technology)
32	Cohen 2003	–	0%	–	17	–	PCR/Restriction enzyme analysis, direct sequencing
33	Burger 2006	–	0%	–	79	–	Allele-specific PCR Direct sequencing
34	Liu 2009	–	0%	–	93	–	PCR/ High resolution DNA melting analysis
35	Köllerman 2010	–	0%	–	43	–	PCR/Sequencing
36	Robinson 2015	–	̴0.6%	%4	150	^#	Whole exome sequencing
37	Beltran 2016	–	1.2%	–	81	^#	Whole exome sequencing
38	Cohn 2017	–	0%	–	23	–	PCR/Direct Sanger Sequencing
39	Jafarian 2018	–	4%	–	100	BRAF V600E	PCR/Direct Sequencing
40	Suh 2020	–	15%	–	20	BRAF K601E**	tNGS (targeted Next Generation Sequencing)
41	Kasajima 2020	–	4.7%	–	21	BRAF K601E	Nucleotide sequencing
42	Müller 2007	–	–	0%	12	–	PCR/SSCP ve automatic nucleotide sequencing
43	Sun 2009	–	–	3%	40	PIK3CA E545A	PCR-SSCP Direct sequencing
44	Boormans 2010	–	–	0%	63	–	PCR/Automatic sequencing
45	Beltran 2013	–	–	4%	45	^#	tNGS
46	Barbieri 2013	–	–	̴4%	112	^#	Exome sequencing
47	Millis 2016	–	–	3.4%	173	PIK3CA E545K H1047R***	NGS
48	Kumar 2016	–	–	̴1.8	54	–	Whole exome sequencing aCGH (Microarray Based Comparative Genomic Hybridization) RNA transcript profiling
49	Huang 2017	–	–	<3%	102	^#	Exome sequencing
50	Rescigno 2018	–	–	6%	418	^#	MiSeqTM based targeted next generation sequencing
51	Dawson 2020	–	–	4.5%	1010	^#	NGS
52	Schultz Loda Sander 2015	^#	2.4%	̴1.8%	333	BRAF Non-V600Ee noncanonical PIK3CA E545K, Q546K, N345I, C420R, E474A, 1 case combined E542A-N345I	Whole exome sequencing
53	Hovelson 2015	^#	^#	^#	114	^#	NGS
54	Grasso 2015	^#	̴1.8%	̴1.8%	53	BRAF V600insHT	NGS qRT-PCR
55	Iacono 2016	–	–	^#	60	^#	NGS
56	Seed 2017	–	–	^#	110	^#	Target amplicon sequencing (Illumina MiSeq platform) Exome sequencing aCGH
57	Barata 2018	^#	^#	^#	66	^#	tNGS
58	Mitri 2018	^#	^#	^#	10	^#	Whole genome sequencing (Illumina NextSeq)
59	Hussain 2018	–	–	̴3.75.	80	^#	Targeted exome sequencing
60	Abida 2019	^#	^#	^#	429	^#	Whole genome sequencing Transcriptome sequencing
61	Zhao 2020	–	^#	–	100	^#	Whole genome bisulfate sequencing Deep whole genome and transcriptome sequencing
62	Crumbaker 2020	^#	^#	^#	13	^#	Deep whole genome sequencing
63	Current	12,5%	0%	0%	24	KRAS 12, 61	PCR/Microarray hybridization (Randox Molecular Diagnostics)

#The detailed codon information and rate of specific mutations are not available especially in NGS-based studies since numerous genetic changes including amplification, deletion, or mutation in multiple gene regions were analyzed simultaneously.

*Codon 12 and 13 are in exon 2; codon 61 is in exon 3. Exon data was given in the article but detailed codon information was not available.

**K601E mutation was found in two of three cases. It was not available codon data of the other case with BRAF mutation.

***The most common codons.

Figure 3. Interaction of intracellular signal transduction pathways and mutation frequency ranges detected in KRAS, BRAF and PIK3CA in human PCa tissues in the literature.