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Supplementary Materials for:
Correlation between gene variants, signaling pathways and efficacy of chemotherapy drugs against
colon cancers
Swarnendu Tripathi,1,2,3,* Louiza Belkacemi,1 Margaret S. Cheung,2,3 and Rathindra N. Bose1
1
Departments of Biology and Biochemistry, University of Houston, Houston Texas, USA. 2Department of Physics, University of Houston,
Houston Texas, USA. 3Center for Theoretical Biological Physics, Rice University, Houston Texas, USA.
* Corresponding author: [email protected]
Figure S1. Venn diagram of the 188 unique genes for which the mutations were analyzed across
the NCI-60 colon cancer cell lines. The number of genes is indicated inside the brackets for
different categories.
Figure S2. GI50 data set and mean graph of PT-112 (NSC # 756765), as obtained from the NCI
Development Therapeutics Program. Note that the GI50 data, only for the NCI-60 cell lines were
used to calculate the z-scores of PT-112 in Figure S3.
Table S1. Relevant information on the NCI-60 colon cancer cell lines as obtained from the
catalogue of somatic mutation (COSMIC) (http://cancer.sanger.ac.uk/cell_lines/cbrowse/nci).
Cell lines
COLO_205
HCC2998
HCT_116
HCT_15
HT_29
KM12
SW620
Primary site
Large
Large
Large
Large
Large
Large
Large
(Subtype1)
Intestine
Intestine
Intestine
Intestine
Intestine
Intestine
Intestine
(Colon)
(Colon)
(Colon)
(Colon)
(Colon)
(Colon)
(Colon)
137
5079
1602
4766
262
1088
241
Number of
mutations
Figure S3. Activity of platinum (Pt) based drugs (PT-112, oxaliplatin, carboplatin and cisplatin)
and 5-FU across the NCI-60 cell lines for nine different cancer types. Drug activity based on the
z-scores were determined from the growth inhibitory 50% (GI50) data (see Methods in the main
text) across the 60 cell lines for 9 different cancer types: BR (breast); CNS (central nervous
system); CO (colon); LE (leukemia); ME (melanoma); LC (lung); OV (ovarian); PR (prostate);
and RE (renal) cancer. The shaded region indicates the z-scores for the seven colon cancer cell
lines.
Table S2. Correlation between cisplatin activity and amino-acid (AA) variants of NCI-60 colon
cancer cell lines (for genes common with oxaliplatin). “X” symbol indicates that the AA variant
is not correlated with drug activity. Other genes (not in common with oxaliplatin) for which the
variant(s) correlate with cisplatin activity are: PI3KCA, CREBBP, FAM123B, HNF1A, NF2, and
PRDM1.
Genes
NF1
COLO_205
KEAP1
MTOR
NOTCH1
MED12
26% (G>A)
P1193L
89% (G>A)
P1377S
HCC2998
HCT_116
HCT_15
53% (C>T)
A2596V
52% (C>T)
A188T
HT_29
X
69% (G>A)
P1581L
100% (G>C)
V312L
46% (G>A)
P1377S
51% (G>A)
Q265*
48% (A>C)
I2500M
46% (A>T)
T2029S
X
KM12
65% (T>G)
L1361R
55% (C>T)
A30T
31% (G>A)
P1254L
SW620
Table S3. Correlation between carboplatin activity and AA-variants (colon cancer) (for genes
common with oxaliplatin). “X” symbol indicates that the AA variant is not correlated with drug
activity. Other genes (not in common with oxaliplatin) for which the variant(s) correlate with
carboplatin activity are: ELF3 EP300; SETD2; ATRX CHEK2 SMC3; ERBB4 FLT3; PIK3CA;
APC; CDH1; LIFR USP9X; BCOR CASP8 CREBBP CYLD FAM123B GNAS MED12 NF2
PRDM1 PTCH1 SMARCA4 TSHR.
Genes
TSHZ3
COLO_205
HCC2998
SIN3A
PBRM1
48% (G>A)
R710*
38% (C>T)
V1267I
ATR
EPHA3
HCT_116
54% (C>T)
A912T
45% (G>A)
P862L
MED12
52% (C>A)
E355D
41% (A>C)
Splicing
KM12
X
X
X
53% (C>T)
A2596V
52% (C>T)
A188T
51% (G>A)
Q265*
26% (G>A)
P1193L
89% (G>A)
P1377S
65% (T>G)
L1361R
55% (C>T)
P1254L
48% (A>C)
I2500M
46% (A>T)
T2029S
SW620
52% (C>G)
K297N
62% (G>T)
M696I
KEAP1
NOTCH1
HT_29
23% (C>T)
R982K
NF1
MTOR
HCT_15
31% (G>A)
P1254L
60% (G>A)
P915L
100% (G>T)
G1807C
69% (G>A)
P1581L
100%
(G>C)
V312L
46% (G>A)
P1377S
Table S4. Summary of biological functions of the uniquely mutated genes for which the aminoacid changing variant(s) exhibits correlation with the activity of oxaliplatin or 5-FU or both for
the colon cancer cell lines. The underlined genes are related with colon cancer progression from
KEGG pathway (http://www.genome.jp/dbget-bin/www_bget?pathway+hsa05210).
Gene
Description
Function
Teashirt zinc finger
Transcriptional regulator involved in developmental processes.
symbol
TSHZ3
TSHZ2
homeobox 3
Teashirt zinc finger
TSHZ2 is a protein-coding gene. Diseases associated with TSHZ2
homeobox 2
include colon cancer. An important paralog of this gene is TSHZ3.
This locus encodes a subunit of ATP-dependent chromatin-
PBRM1
Polybromo 1
remodeling complexes. The encoded protein an integral
component of complexes necessary for ligand-dependent
transcriptional activation by nuclear hormone receptors.
The protein is a member of the Polycomb group of proteins, which
ASXL1
Additional sex combs
are necessary for the maintenance of stable repression of homeotic
like 1 (Drosophila)
and other loci. ASXL1 mutations are a prognostic biomarker,
associated with shorter overall survival.1 Drugs targeting the
spliceosome are in development to inhibit cancer progression.
ATR is a serine/threonine kinase that belongs to the
phosphoinositide 3- kinase related protein kinases (PIKKs),
particularly to ATM (ataxia telangiectasia mutated) subfamily. It
ATR
Ataxia telangiectasia
functions to maintain genome integrity by stabilizing replication
and Rad3 related
forks and by regulating cell cycle progression and DNA repair.
ATR has been proposed to serve as a haplo insufficient tumor
suppressor in some types of cell deficiencies and its activation has
been detected in most cancer chemotherapies.
This gene belongs to the ephrin receptor subfamily of the
EPHA3
protein-tyrosine kinase family. EphA3 may play an important
EPH receptor A3
role in the development and progression of tumours, and thus
become useful indicators for clinical assessment of tumour
biological behaviour and prognosis in patients with colorectal
carcinoma.2
It is an autosomal-dominant inherited tumor syndrome in which
NF1
affected individuals are prone to the development of both benign
and malignant tumors.3
Notch signaling is an evolutionarily conserved pathway that
regulates critical cellular pathways and plays a key role in the
development of normal tissues and cell through various effects on
differentiation, proliferation, cell fate decision and stem cell
NOTCH1
renewal potential. Aberrantly activated Notch signaling plays a
key role in carcinogenesis and progression of human malignancy.
Notch1 as prognostic predictor and therapeutic target, both of
which are relevant to practice in clinical oncology.4
POLQ is a specialized DNA polymerase. POLQ has been
implicated in the defense against genomic instability, in base
POLQ
excision repair. Retrospective studies of clinical samples show
that higher levels of POLQ gene expression in colorectal cancer
are correlated with poorer outcomes for patients.5
MutL homolog 1
MLH1
A molecular phenotype associated with microsatellite instability
(MSI), represents a consistent feature of tumors from patients with
hereditary nonpolyposis colorectal cancer.3
Ring finger protein 34
RNF43
RNF43 encodes an E3 ubiquitin ligase that negatively regulates
Wnt signaling. RNF43 is one of the most commonly mutated
genes in colorectal.6
IDH1
KEAP1
Isocitrate
Aberrant mRNA expression of IDH1 gene might be actively
dehydrogenase 1
involved in the development of colon cancer.7
Kelch-like ECH-
Aberrant methylation of the KEAP1 gene promoter is emerging as
associated protein 1
a main mechanism of dysregulation of the NrF2 (nuclear factorerythroid 2-related factor 2) which plays a pivotal role in the
cellular response to oxidative stress.
KRAS
V-Ki-ras2 Kirsten rat
KRas is a protein that in humans is encoded by the KRAS gene.
sarcoma viral oncogene
KRAS is highly mutated in colon cancer. Detailed description is
given in the manuscript.
MECOM
MDS1 and EVI1
The protein encoded by this gene is a transcriptional regulator and
complex locus
oncoprotein that may be involved in hematopoiesis, apoptosis,
development, and cell differentiation and proliferation.
MTOR
Mammalian target of
mTOR is frequently activated in colon cancer due to mutations in
rapamycin (mTOR)
the phosphatidylinositol 3-kinase (PI3K) pathway. Targeting
mTOR with allosteric inhibitors of mTOR such as rapamycin
reduces colon cancer progression in several experimental models.
NCOR1
Nuclear receptor
This gene encodes a protein that mediates ligand-independent
corepressor 1
transcription repression of thyroid-hormone and retinoic-acid
receptors by promoting chromatin condensation and preventing
access of the transcription machinery.
PPP2R1A
Protein phosphatase 2,
This gene encodes a constant regulatory subunit of protein
regulatory subunit A,
phosphatase 2. Protein phosphatase 2 is one of the four major
alpha
Ser/Thr phosphatases, and it is implicated in the negative control
of cell growth and division.
RAD21 is a component of the cohesion complex and is integral to
chromosome segregation and error-free DNA repair. RAD21 is
functionally important in tumor progression but its role in
RAD21
colorectal carcinoma is unclear. Rad21 as a gatekeeper of LOH
and a β-catenin target gene and provide evidence that Wnt
pathway activation drives RAD21 expression in human colon
cancer.
The protein encoded by this gene is a negative regulator of the cell
RB1
Rinoblastoma 1
cycle and was the first tumor suppressor gene found. The encoded
protein also stabilizes constitutive heterochromatin to maintain the
overall chromatin structure.
This protein is a histone methyltransferase that is specific for
SETD2
SET domain containing
lysine-36 of histone H3, and methylation of this residue is
2
associated with active chromatin. This protein also contains a
novel transcriptional activation domain and has been found
associated with hyperphosphorylated RNA polymerase II
SIN3A
Transcription regulator
The protein encoded by this gene is a transcriptional regulatory
family member A
protein.
Structural maintenance
This gene belongs to the SMC3 subfamily of SMC proteins. The
of chromosomes 3
encoded protein occurs in certain cell types as either an
intracellular, nuclear protein or a secreted protein. The nuclear
SMC3
form, known as structural maintenance of chromosomes 3, is a
component of the multimeric cohesin complex that holds together
sister chromatids during mitosis, enabling proper chromosome
segregation.
This gene encodes a member of the Ser/Thr protein kinase family
and the TGFB receptor subfamily. The encoded protein is a
transmembrane protein that has a protein kinase domain, forms a
TGFBR2
Transforming growth
heterodimeric complex with another receptor protein, and binds
factor, beta receptor II
TGF-. This receptor/ligand complex phosphorylates proteins,
which then enter the nucleus and regulate the transcription of a
subset of genes related to cell proliferation.
ARID2
AT rich interactive
ARID2 is a subunit of the PBAF chromatin-remodeling complex,
domain 2
which facilitates ligand-dependent transcriptional activation by
nuclear receptors.8
This gene encodes a cytoplasmic protein that contains a regulation
of G-protein signaling (RGS) domain and a dishevelled and axin
(DIX) domain. The encoded protein interacts with adenomatosis
AXIN1
Axin 1
polyposis coli, catenin beta-1, glycogen synthase kinase 3 beta,
protein phosphate 2, and itself. This protein functions as a
negative regulator of the wingless-type MMTV integration site
family, member 1 (WNT) signaling pathway and can induce
apoptosis.
The protein encoded by this gene was identified as an interacting
corepressor of BCL6, a POZ/zinc finger transcription repressor
that is required for germinal center formation and may influence
BCOR
BCL6 corepressor
apoptosis. This protein selectively interacts with the POZ domain
of BCL6, but not with eight other POZ proteins. Specific class I
and II histone deacetylases (HDACs) have been shown to interact
with this protein, which suggests a possible link between the two
classes of HDACs.
The protein encoded by this gene belongs to the membrane-
CARD11
Caspase recruitment
associated guanylate kinase (MAGUK) family, a class of proteins
domain family, member
that function as molecular scaffolds for the assembly of
11
multiprotein complexes at specialized regions of the plasma
membrane.
CIC
HNF1A
Capicua transcriptional
repressor
HNF1 homeobox A
The protein encoded by this gene is a transcription factor.
The protein encoded by this gene is a member of the Janus kinase
JAK3
Janus Kinase 3
(JAK) family of tyrosine kinases involved in cytokine receptormediated intracellular signal transduction.
Initiation of transcription is controlled in part by a large protein
assembly; the preinitiation complex. A component of this complex
MED12
Mediator complex
is a 1.2 MDa protein aggregate called Mediator. This Mediator
subunit 12
component binds with a CDK8 subcomplex which contains the
protein encoded by this gene, mediator complex subunit 12
(MED12), along with MED13, CDK8 kinase, and cyclin C. The
CDK8 subcomplex modulates Mediator-polymerase II interactions
and thereby regulates transcription initiation and reinitation rates
The protein encoded by this gene is a G protein-coupled receptor
SMO
Smoothened, frizzled
that interacts with the patched protein, a receptor for hedgehog
family receptor
proteins. The encoded protein transduces signals to other proteins
after activation by a hedgehog protein/patched protein complex.
This gene was identified as a gene whose expression is rapidly
induced by the tumor necrosis factor (TNF). The protein encoded
TNFAIP3
Tumor necrosis factor,
by this gene is a zinc finger protein and ubiqitin-editing enzyme,
alpha-induced protein 3
and has been shown to inhibit NF-kappa B activation as well as
TNF-mediated apoptosis. The encoded protein is involved in the
cytokine-mediated immune and inflammatory responses.
Table S5. List of driver genes that exhibit non-synonymous mutations across the NCI-60 cell
lines (see Figure 1 and 2 in the Main text).
Signaling
pathways/
Cellular
Process
Transcription
factor/regulator
Histone
modifier
Genome
integrity
RTK signaling
Cell cycle
MAPK
signaling
PI(3)K
signaling
TGF-β
signaling
Driver
genes
VHL
GATA3
EP300
RUNX1
WT1
PHF6
SOX9
MLL3
ARID1A
PBRM1
SETD2
SETBP1
KDM5C
KDM6A
ASXL1
EZH2
TP53
ATM
ATRX
BRCA2
STAG2
BAP1
BRCA1
EGFR
FLT3
PDGFRA
FGFR2
FGFR3
CDKN2A
RB1
KRAS
NF1
MAP3K1
BRAF
NRAS
PIK3CA
PTEN
PIK3R1
SMAD4
ACVR1B
SMAD2
Wnt/β
-catenin
signaling
Proteolysis
Splicing
HIPPO
signaling
DNA
methylation
Metabolism
NFE2L
Protein
phosphatase
Other
Cell survival
APC
CTNNB1
FBXW7
SPOP
SF3B1
U2AF1
CDH1
DNMT3A
TET2
IDH1
NFE2L2
PPP2R1A
PTPN11
NOTCH1
NCOR1
AR
ABL1
ALK
B2M
CARD11
CASP8
CBL
CDC73
CIC
CSF1R
CYLD
ERBB2
GNA11
GNAQ
GNAS
HRAS
JAK1
JAK2
JAK3
MAP2K1
MED12
MET
MPL
MYD88
RET
SOCS1
TNFAIP3
TRAF7
TSC1
TSHR
Cell fate
Genome
maintanence
ARID1B
ARID2
AXIN1
BCOR
CREBBP
DNMT1
FAM123B
GATA1
GATA2
HNF1A
KLF4
MEN1
NF2
NOTCH2
PAX5
PRDM1
PTCH1
RNF43
SMARCA4
SMARCB1
SMO
MLH1
MSH2
MSH6
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