Download SupplementaryFigures 1-4 - Cancer Prevention Research

Supplemental Figure 1
SSA/Ps Syndromic
SSA/Ps Sporadic
63
284
9
342
236
600
124
HPs Sporadic
Genes differentially expressed ≥ 2-fold in syndromic and sporadic SSA/Ps and
hyperplastic polyps by RNA sequencing. Differentially expressed genes with ≥ 2fold change and FDR < 0.05 in syndromic SSA/Ps (n=12), sporadic SSA/Ps (n=9) and
HPs (n=10) compared to control colon. Syndromic and sporadic SSA/Ps were
compared to control right colon (n=10) and HPs were compared to control left colon
(n=10). 1350, 698 and 711 genes were differentially expressed in syndromic and
sporadic SSA/Ps and HPs, respectively. 1422 genes total were differentially
expressed in syndromic and/or sporadic SSA/Ps.
SporadicRight_2
SyndromicRight_5
SyndromicRight_1
SyndromicRight_2
SporadicRight_1
SporadicLeft_2
SyndromicRight_3
SyndromicRight_4
ControlRight_6
SporadicLeft_1
SyndromicLeft_1
ControlRight_10
ControlRight_4
ControlRight_9
ControlRight_8
ControlRight_1
ControlRight_3
ControlRight_5
ControlRight_7
ControlRight_2
Supplemental Figure 2
Log2 Ratio
Color Bar
Comparison of gene expression in uninvolved colon from patients with
SSA/Ps with control colon from patients without polyps. Relative expression
of 1922 genes found differentially expressed (Fold ≥ 2 and FDR < 0.01) between
uninvolved (n=10, 7 right and 3 left) and control right colon (n=10). Uninvolved
colon includes six uninvolved colon from syndromic patients with SSA/Ps and four
uninvolved colon from sporadic patients with SSA/Ps. Log2 ratios comparing each
individual sample to the mean of 10 right control colon samples was used for
hierarchical clustering.
Supplemental Figure 3
Log2 Ratio
Color Bar
Evaluation of an SSA/P gene signature using previously published microarray data of
SSA/Ps, MVHPs and control colon. Quantile normalized expression data for each signature
gene was downloaded from the Gene Expression Omnibus (GEO) under accession number
GSE43841. Expression data from six SSA/Ps, six MVHPs and six control colon FFPE samples
(three right and three left) was evaluated for expression of our gene markers. Hierarchical
clustering of log2 ratio values comparing each individual colon sample (SSA/P – sessile
serrated adenoma/polyp, MVHP – microvesicular hyperplastic polyp, CTRL – control colon) to
the mean of all 18 colon samples is shown. Red and green denote overexpression and
underexpression, respectively. Clustering was performed using a correlation metric and
complete linkage.
Supplemental Figure 4
mRNA expression of four SSA/P signature genes (FSCN1, MUC6, SEMG1 and ZIC5) in
SSA/Ps, HPs, uninvolved colon and control colon by quantitative RT-PCR (qPCR). mRNA
expression for each gene was determined using commercially available TaqMan gene
expression assays (Invitrogen) and a Applied Biosystems 7900HT real-time PCR instrument.
10ul qPCR reactions were performed with forward and reverse primers, internal probe, master
mix and 10-15 ng cDNA. cDNA was made from total RNA using the High Capacity RNA to
cDNA kit (Invitrogen). A total of 73 samples were analyzed, 21 SSA/Ps, 12 HPs, 17 uninvolved
and 23 control colon. Beta-actin was used a reference and control colon as the baseline for
determining fold change using the ΔΔCT method. Statistical significance was determined by the
non-parametric Mann Whitney U test.