DNA polymerase epsilon-mutant colorectal cancers: Insights into non-exonuclease domain mutation variants, microsatellite instability status, and co-mutation profiles

Table 1 Clinical and pathological features of DNA polymerase epsilon-mutant colorectal cancer patients, n (%)/mean ± SD

Characteristics	Value
Gendera
Female	69 (36.13)
Male	122 (63.87)
Age at diagnosis, years	mean ± SD
Female	63.6 ± 12.3
Male	66.6 ± 10.2
All POLE-mutant CRC patients	65.5 ± 11.1
Differentiation degreea
Well differentiated	80 (41.88)
Moderately differentiated	73 (38.22)
Poorly differentiated	38 (19.90)
Localizationa
Colon	160 (83.77)
Rectum	31 (16.23)

^aP < 0.01.

CRC: Colorectal cancer; POLE: DNA polymerase epsilon.

Table 2 The DNA polymerase epsilon exonuclease domain mutations and non-exonuclease domain mutations observed in colorectal cancer patients

POLE mutation	Exon	Nucleotide substitution	Protein change	Mutation type	Clinical significance
Non-EDM	34	c.4337_4338delTG	p.V1446fs*3	Microsatellite (frameshift)	Conflicting classifications of pathogenicity
EDM	14	c.1373A>T	p.Y458F	Nonsense	Pathogenic
EDM	14	c.1402T>A	p.Y468N	Missense	Uncertain significance
Non-EDM	17	c.1834G>A	p.D612N	Missense	Uncertain significance
Non-EDM	42	c.5725C>T	p.R1909	Nonsense	Pathogenic
Non-EDM	15	c.1551delC	p.N518fs*10	Deletion	Pathogenic
Non-EDM	41	c.5653G>A	p.A1885T	Frameshift	Uncertain significance
Non-EDM	29	c.3510dupA	p.L1171fs*6	Duplication	Pathogenic
Non-EDM	39	c.5320C>T	p.Q1774*	Nonsense	Pathogenic
Non-EDM	24	c.2731C>T	p.Q911*	Nonsense	Pathogenic

EDM: Exonuclease domain mutation; POLE: DNA polymerase epsilon.

Table 3 Variants accompanying DNA polymerase epsilon mutations in colorectal cancer patients

POLE mutations	Gene	Nucleotide substitution	Protein change
	APC	c.994C>T, c.646C>T, c.4348C>T, c.1690C>T, c.4192_4193delAG, c.4729G>T	p.R332*, p.R216*, p.R1450*, p.R564*, p.R1399fs*9, p.E1577*
	ASXL1	c.1188_1201delGCGTGGTGGT	p.Q396fs*9
	AXIN2	c.1195C>T	p.R399*
	BAX	c.763A>T, c.121dupG	p.I255F, p.E41fs*33
	BLM	c.1544delA	p.N515fs*16
	BRAF	c.1742A>T, c.2141T>A, c.1799T>A, c.2102G>T, c.1406G>C, c.1790T>A	p.N581I, p.I714N, p.V600E, p.R701I, p.G469A, p.L597Q
	BRCA1	c.1961delA, c.66dupA	p.K654fs*47, p.E23fs*18
Non-EDM	BRCA2	c.1813delA, c.5073delA, c.7007G>A, c.9072_9092delCAAC, c.9097delA	p.I605fs*9, p.K1691fs*15, p.R2336H, p.N3024_T3030, p.T3033fs*29
	CDH1	c.549_554delCAAAGA, c.944dupA	p.D183 K184del, p.N315fs*6
	CEBPA	c.564_566delGCC	p.P189del
	CHEK2	c.1556C>T, c.562C>T	p.T519M, p.R188W
	CREBBP	c.5837delC	p.P1946fs*30
	EGFR	c.2236_2250delGAATTAAG, c.2174C>T, c.2509G>A	p.E746_A750del, p.T725M, p.D837N
	EP300	c.4408delA, c.6370dupG, c.4408delA, c.1425dupT	p.M1470fs*26, p.V2124fs*86, p.M1470fs*26, p.Q476fs*37
	ERBB2	c.2524G>A	p.V842I
	ERCC5	c.2751delA	p.K917fs*65
	FBXW7	c.1436G>A	p.R479Q
	FGFR1	c.396_398delTGA	p.D133del
	FGFR3	c.1148delA, c.2128G>A, c.1150T>C	p.F383S, p.G710S, p.F384 L
	FLT4	c.1267delC	p.Q423fs*70
	IDH1	c.394C>T	p.R132C
	IDH2	c.419G>A	p.R140Q
	JAK2	c.515G>A	p.R172Q
	JAK3	c.1849G>T	p.V617F
	KIT	c.1880C>T, c.2447A>T	p.P627 L, p.D816V
	KRAS	c.38G>A, c.35G>C, c.182A>G, c.35G>A, c.35G>T, c.351A>C	p.G13D, p.G12A, p.Q61R, p.G12D, p.G12V, p.K117N
	MLH1	c.676C>T	p.R226*
	MLH3	c.2116delA, c.1755delA	p.T706fs28, p.E586fs*24
	MSH3	c.1148delA	p.K383fs*32
	MSH6	c.2314C>T, c.3261dupC	p.R772W, p.F1088fs*32
	NRAS	c.34G>T, c.182A>T, c.35G>A, c.38G>A	p.G12C, p.Q61 L, p.G12D, p.G13D
	PALB2	c.3201+1G>A	p.?
	PIK3CA	c.1634A>G, c.3140A>T, c.331A>G	p.E545G, p.H1047 L, p.K111E
	PIK3R1	c.244delA, c.1690A>G	p.I82fs*32, p.N564D
	PMA2	c.1239delA	p.D414fs*34
	PMS2	c.1239delA, c.630dupA	p.D414fs*34, p.R211fs*38
	POLD1	c.347delC	p.P116fs*53
	POLD3	c.898delA	p.R300fs*5
	PTEN	c.19G>T, c.407G>A, c.802-2delA, c.802-2A>T, c.397G>A	p.E7*, p.C136Y, p.?, p.?, p.V133I
	RET	c.1900T>A	p.C634S
	SMAD4	c.1094G>T	p.G365V
	TCF7 L2	c.1385delA, c.1403delA	p.K462fs*23, p.K468fs*23
	TGFBR2	c.383dupA	p.P129fs*3
EDM	MLH3	c.2116delA, c.1755delA	p.T706fs28, p.E586fs*24
	MSH3	c.1148delA	p.K383fs*32

?: Unknown.

Table 4 Distribution of DNA polymerase epsilon mutation type and microsatellite instability status

POLE mutation type	Total patients (n)	MSI-H (n)	MSS/MSI-L (n)	P value
EDM mutation	2	0	2
Non-EDM mutation	189	23	166
Total	191	23	168	P = 1.0

EDM: Exonuclease domain mutation; MSI-H: High microsatellite instability; MSI-L: Low microsatellite instability; MSS: Microsatellite-stable; POLE: DNA polymerase epsilon.

Table 5 Stratified descriptive statistics of DNA polymerase epsilon-mutant colorectal cancer patients by age, tumor location, and microsatellite instability status, including all co-mutations, n (%)

POLE mutation	Patient (n)	MSI-H	MSS/MSI-L	Co-mutation	OR MSI-H	95%CI	Colon (n)	Rectum (n)	Age (n)
									< 50 years	50-65 years	> 65 years
EDM	2	0 (0)	2 (100)	-	0.03	0.001 to -1.2	2	0	1	1	0
Non-EDM	189	23 (12.17)	166 (87.83)	BRAF, ERCC5, KRAS, MLH3, MSH3, MSH6, PIK3CA, PMS2, TCF7 L2, TP53	1 (reference)	-	150	39	50	100	39
Total	191	23 (12.04)	168 (87.96)	-	-	-	152	39	51	101	39

The most frequent 10 co-mutations are listed. CI: Confidence interval; EDM: Exonuclease domain mutation; MSI: Microsatellite instability; MSI-H: High microsatellite instability; MSI-L: Low microsatellite instability; MSS: Microsatellite-stable; OR: Odds ratio; POLE: DNA polymerase epsilon.