The Potential Role of Genomic Signature in Stage II Relapsed Colorectal Cancer (CRC) Patients: A Mono-Institutional Study

Figures & data

Figure 1 CONSORT 2010 flow diagram.

Figure 2 The Cancer Genome Atlas Colon Adenocarcinoma Cohorts (TCGA COAD) stage II CRCs.

Figure 3 The Cancer Genome Atlas Colon Adenocarcinoma Cohorts (TCGA COAD) stage II non recurred CRCs.

Figure 4 The Cancer Genome Atlas Colon Adenocarcinoma Cohorts (TCGA COAD) stage II recurred CRCs.

Table 1 Clinicopathologic Features of Patients

Clinicopathologic Features (Valid Cases and Percentages)
		N.	%
Total		17	100
Follow up time
Median (range min-max)	60 (4–107)
Age
Median (range min-max)	71 (43–84)
<70 years		7	41
≥70 years		10	59
Sex
Male		14	82
Female		3	18
Tumour location
Right-side colon		12	71
Left-side colon		5	29
pT stage
T3		14	82
T4		3	17
N. of Lymph-node retrieved
<12		1	6
≥12		16	94
Lymphovascular/Perineural invasion (n=14)
Not		7	67
Yes		4	35
Tumour differentiation (grading)
G2		11	65
G3		6	35
Histopathological Stage risk
Low		9	53
High		8	47
Relapse
Oligometastatic		8	47
Multiple metastases		9	53
Local Recurrence		1	6
Distant recurrence		14	82
Liver		5	36
Lung		5	36
Bone		2	14
Lymph-nodes		2	14
Abdominal wall		1	7
Microsatellite Instability
MSS		14	82
MSI-H (BRAF mut)		3 (3)	18 (100)
CDX2 expression
Positive		16	94
Negative		1	6
Tumor budding (n=16)
Low/absent		8	50
High		8	50
Adjuvant CT
Nil		11	65
Oral capecitabine		3	18
FOLFOX		3	18

Abbreviations: MSS, microsatellite status stable; MSI-H, microsatellite status instable-high; BRAF mut, BRAF mutation; CT, chemotherapy; Nil, not done.

Table 2 Genomic Profile and Clinicopathological Characteristics of Relapsed CRC Patients

Patient Number	Sex	Age	Number of Genes	Genes	Sidedness CRC	Site of Recurrance	MMR Status	Risk	Adj CT	mDFS	mOS
01	M	71	14	APC, TP53 KRASMLH1 ARID2, CIC KMT2C SOX9, MSH2 CDKN1B EPHA5 MED12 PTCH1 RUNX1	R	Lung	MSI	High	None	12	19
02	F	77	10	APC, TP53 KRAS KMT2C ASXL1 CDK8, IRS2 CEBPA EGF14, FLT3	R	Lung	MSS	High	None	10	65
03	F	75	10	PIK3CA MLH1 PTEN LRPB1 RNF43 SOX9, ATM CTNNA1 FANCA	R	Liver	MSI	Low	Cape	16	46
04	M	69	10	APC, TP53 NRAS AURKA BCL2L1 GNAS, TOP1 KEL, SRC ZNF217	R	Liver	MSS	Low	None	40	57
05	M	76	7	APC, TP53 PIK3CA FBXW7 ARID2 EGFR, EZH2	R	Lung	MSS	Low	None	4	4
06	M	84	7	APC, TP53 PIK3CA KMT2C FAM123B FGFR1, NF1	R	Lung	MSS	Low	None	14	49
07	M	69	6	AP, BRAF FBXW7 SMAD4 AKT1, GRM3	R	Lymph-nodes	MSI	Low	Folfox	11	17
08	M	70	6	APC, TP53 BCL2L1 ERBB4 SPTA1, SRC	L	Bone	MSS	High	Folfox	25	30
09	M	74	6	APC, TP53 KRAS, FLCN BCL2L2 MYST3	R	Liver, lymphnodes	MSS	Low	None	45	65
10	M	58	6	KRAS, MLL2 MLH1, CIC RNF43 CTNNB1	L	Local	MSI	Low	Cape	54	63
11	M	82	5	APC, KRAS LRP1B ERBB4 MAP2K4	R	Bone, lymphnodes	MSS	High	None	14	53
12	F	75	5	APC, KRAS BRCA2 NF2, SF3B1	L	Liver	MSS	Low	None	14	77
13	M	68	5	APC, TP53 FBXW7 NRAS CHD1	L	Lung	MSS	High	Folfox	23	54
14	M	69	5	APC, TP53 PIK3CA PTEN ARID1A	R	Liver	MSS	Low	None	30	37
15	M	62	5	APC, TP53 KRAS SMAD4 PIK3CG	R	Abdominal wall	MSS	Low	Cape	31	81
16	M	43	3	APC, KRAS PIK3CA	L	Liver	MSS	Low	None	10	107
17	M	75	2	TP53, KRAS	R	Lung	MSS	High	None	4	21

Abbreviations: M, male; F, female; CRC, colorectal cancer; R, right; L, left; MMR, mismatch repair; MSS, microsatellite status stable; MSI, microsatellite status instable; Adj CT, adjuvant chemotherapy; mDFS, median disease-free survival; mOS, median overall survival.

Figure 5 Frequency and representation of gene mutations in cohort study. Vertical axis: frequency of mutations. Horizontal axis: genes.

Figure 6 STRING network analysis of relevant gene mutations (N=17 patients). *Log10 (observed/expected). This measure describes how large the enrichment effect is. It’s the ratio between i) the number of proteins in your network that are annotated with a term and ii) the number of proteins that we expect to be annotated with this term in a random network of the same size. ^#This measure describes how significant the enrichment is. Shown are p-values corrected for multiple testing within each category using the Benjamini–Hochberg procedure.

Notes: Color of edges represents protein-protein associations. Known interactions: pink: experimentally determined; turquoise: from curated databases. Predicted interactions: green: gene neighborhood; red: gene fusions; blue: gene co-occurrence. Others interactions: yellow: text mining; black: co-expression; light blue: protein homology. Color of balls represents biological process in which genes are involved as showed in figure above.

Table 3 Univariate Analysis for Disease Free Survival (DFS) and Overall Survival (OS)

	Disease Free Survival		Overall Survival
Variables	Median Months	HR (95% CI)	Median Months	HR (95% CI)
Sex F v M	14 v 14	2.0 (0.5–7.9)	65 v 81	1.0 (0.2–5.3)
Age >70 v ≤70	14 v 30	2.1 (0.7–6.0)	46 v 81	2.3 (0.5–11.6)
Colon right v left	14 v 23	1.5 (0.5–4.8)	46 v NR	4.7 (0.6–37.5)
Risk high v low	12 v 16	2.4 (0.7–7.6)	30 v 81	2.2 (0.5–9.0)
Recurrence lung v liver v other	10 v 16 v 25	3.9 (1.0–14.4)	21 v NR v 81	3.9 (0.6–22.2)
Tumor pT4 v p3	10 v 14	2.8 (0.7–10.7)	65 v 81	1.5 (0.3–7.3)
LVI/PnI yes v not	10 v 25	4.1 (0.8–18.9)	21v 46	1.5 (0.3–6.9)
Grade G3 v G2	14 v 14	1.3 (0.4–3.7)	30 v 81	1.7 (0.4–7.5)
Microsatellite MSI v MSS	12 v 14	1.4 (0.4–5.2	19 v 81	3.2 (0.7–14.6)
Tumor budding high v low	14 v 14	1.7 (0.6–5.1)	65 v 46	1.3 (0.3–4.7)
APC mut v wt	14 v 16	1.9 (0.4–8.6)	81 v 46	0.6 (0.1–2.8)
TP53 mut v wt	23 v 14	1.0 (0.4–3.0)	65 v NR	2.3 (0.5–11.3)
KRAS mut v wt	14 v 16	1.2 (0.4–3.5)	81 v 37	0.3 (0.1–1.5)
PIK3CA mut v wt	14 v 14	1.9 (0.6–6.0)	46 v 65	1.2 (0.3–4.7)
FBXW7 mut v wt	11 v 14	2.6 (0.7–9.9)	17 v 81	3.7 (0.7–19.9)
MLH1 mut v wt	16 v 14	0.5 (0.1–2.1)	46 v 81	1.9 (0.4–9.9)
TP53-KRAS mut v wt	12 v 14	1.0 (0.4–3.2)	65 v NR	1.5 (0.4–6.1)
TP53-PIK3CA mut v wt	14 v 14	1.5 (0.4–5.6)	37 v 81	2.5 (0.5–12.7)
TP53-FBXW7 mut v wt	4 v 14	2.1 (0.4–9.7)	4 v 65	1.9 (0.2–15.8)
N. genetic mutations >6 v ≥6	12 v 23	1.7 (0.6–4.9)	46 v 81	2.2 (0.5–9.0)

Abbreviations: M, male; F, female; mut, mutate; wt, wild type.