Supplement

In an effort to compare our results to a commercially available assay for predicting CC recurrence, we analyzed genes normally used to compute the ColoPrint Assay, in order to explore if the expression of these genes could differentiate the recurrent from non-recurrent patients in our prospective study cohort. The 13 genes comprising the ColoPrint Assay Colon Cancer recurrence score are: EDEM1, THNSL2, LAMA3, HSD3B1, PLIN3, PPARA, ZBED4, LIF, PIM3, MCTP1, CTSC, IL2RB, and IL2RA. These 13 genes selected are present in MicroArray Quality Control (MAQC) and have good expression levels. There was no clear pattern between the expression of these genes and disease-free survival in our analysis (Supplementary Figure 1).Supplementary Tables 1 and 2 show the demographics of our study cohort and the genes comprising the genetic signature.

Supplementary Figure 1: Colon tumor samples grouped by disease relapse against differentially expressed genes. The x-axis represents 113 colon tumor samples and the y-axis represents the list of 13 differentially expressed genes that comprise the Coloprint Assay. These 13 genes are present in (MicroArray Quality Control) MAQC and have good expression levels. The green colors represent gene down-regulation and the red up-regulation. Relapses, at the bottom of the graphic, are denoted by a blue box while a yellow box indicates disease-free survival at 3 years. In our analysis, there was no clear pattern between the expression of these genes and disease-free survival.

Supplementary Table 1. Patient cohort demographics

Total (n=113)
Characteristic / No. / Percent
Mean age (years) / 68.4 ± 13.5
Gender, male / 59 / 52.2
Gender, female / 54 / 47.8
Right colon tumor / 39 / 34.5
Transverse colon tumor / 8 / 7.1
Left colon tumor / 14 / 12.4
Rectosigmoid tumor / 52 / 46.0
Segmental colectomy / 109 / 96.5
>Segmental colectomy / 4 / 3.5
T1 / 13 / 11.5
T2 / 19 / 16.8
T3 / 77 / 68.1
T4 / 4 / 3.5
N0 / 82 / 72.5
N1 / 22 / 19.5
N2 / 9 / 8.0
Recurrence within 3 years / 13 / 11.5
Mean total LNs identified (median) / 20.4 ± 9.64 (18)
Cellular Proliferation Genes
Up-regulated / 11 / 9.7
Down-regulated / 35 / 31.0
No difference relative to control / 67 / 59.3
Stromal (Pro-differentiation) Genes
Up-regulated / 9 / 8.0
Down-regulated / 27 / 23.9
No difference relative to control / 77 / 68.1

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Supplementary Table 2. Genes comprising the recurrent genetic signature

Gene / Sequence Description / GOA Function / GOA Process / Heat map category/GOA component
Stromal-associated Genes / CXCL12 / Chemokine (C-X-C motif) ligand 12 (stromal cell-derived factor 1) / CXCR chemokine receptor binding / Cell adhesion, cell chemotaxis, immune response, G-protein coupled receptor signaling pathway / Stromal and immunoreactive markers, extracellular space
EFEMP1 / EGF-containing fibulin-like extracellular matrix protein 1 / Calcium ion biding, EGFR binding / Extracellular matrix organization / Stromal, colocalizes with extracellular matrix
FBLN1 / Fibulin 1 / Calcium binding, ECM structural constituent / Extracellular matrix organization / Stromal, extracellular space
MFAP5 / Microfibrillar associated protein 5 / ECM structural constituent / Extracellular fibril organization, extracellular matrix organization / Stromal, extracellular region, microfilament
PTGIS / Prostaglandin 12 (prostacyclin) synthase / Heme binding, iron ion binding / Apoptotic signaling pathway / Stromal, extracellular space
Proliferative Genes / RRM2 / Homo sapiens ribonucleotide reductase M2 (RRM2), transcript variant 2, mRNA / Metal ion binding / DNA replication, G1/S transition of mitotic cell cycle, mitotic cell cycle / Cell cycle, cytosol or nucleoplasm
SHCBP1 / SHC SH2-domain binding protein 1 / SH2 domain binding / FGF signaling pathway, regulation of neural precursor cell proliferation / Cell growth
POC1A / WD repeat domain 51A / Protein binding / Cell projection organization / Cell cycle progression, cell division process
ME1 / Malic enzyme 1, NADP(+)-dependent cyctosolic / NAD binding, NADP binding, malic enzyme activity, manganese ion binding, metal ion binding / Malate metabolic process, response to hormones / Stromal, cytoplasmic, mitochondrion

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