Supplementary Information

Network-based combinatorial CRISPR-Cas9 screens

identify synergistic modules in human cells

Yucheng Guo#, Chen Bao#, Dachen Ma, Yubing Cao, Yanda Li, Zhen Xie*, Shao Li*

MOE Key Laboratory of Bioinformatics and TCM-X Center / Bioinformatics Division /

TFIDT, BNRist, Department of Automation, Tsinghua University, Beijing 100084,

China

* Corresponding authors: shaoli@mail.tsinghua.edu.cn, zhenxie@tsinghua.edu.cn.

Contents
S1 Experimental methods

S1.1 Guide RNA library construction

S1.2 Genome extraction and NGS library preparation

S1.3 Hierarchical Assembly of the dual-gRNA knockout library

S1.4 Gene selection, design and synthesis of sgRNAs

S1.5 Lentivirus packaging and infection

S1.6 Verification by RNA interference

S2 Computational methods

S2.1 Determination of sgRNA Phenotypes from Pooled Screens

S2.2 Definitions for Expected Double-sgRNA Phenotypes

S2.3 Synergistic Module-based Drug Prediction

S3 Supplementary Figures

S4 Supplementary Tables

1
S1 Experimental methods
S1.1 Guide RNA library construction
The double gRNA expression library was constructed using a two-step Golden

Gate assembly strategy. The guide RNA target sequences for the 84 genes were

designed using the CRISPR-ERA website. The control target sequences were

scrambled and had no target sites in the genome. The two oligos for each guide RNA

target sequence were synthesized (Genwiz), annealed to form the DNA duplexes

shown in Table S1, and phosphorylated by T4 PNK (NEB). We inserted the

phosphorylated DNA fragment into the first gRNA scaffold constructs (pDC002) driven

by the U6 polymerase III promoter and the second gRNA scaffold constructs (pDC007)

driven by the 7SK polymerase III promoter using the standard Golden Gate assembly

protocol.

To realize the expression of two randomized combinations of guide RNAs, we

constructed second-step cloning products by inserting the U6 driving sgRNA and 7SK

driving sgRNA fragments into the final lentiviral vector (pDC005) encoding the EYFP

fluorescence and puromycin-resistance genes. The plasmid sequences are listed in

Table S2.

S1.2 Genome extraction and NGS library preparation

Genomic DNA was extracted from harvested cells using a genome extraction kit

(Tiangen). The dual gRNA cassette was amplified for paired-end 250-bp deep

sequencing using the primers listed in Table S3.

S1.3 Hierarchical Assembly of the dual-gRNA knockout library

To obtain a construct containing the two-guide RNA-DNA vector library based on

the Golden Gate cloning method, we used a hierarchical strategy (Fig. S2). We first

designed three different gRNAs for each gene. The oligo pairs encoding the guide

RNA targeted sequence were synthesized, annealed and phosphorylated. To enable

the simultaneous expression of two guide RNAs in one vector, the annealed and

phosphorylated DNA fragment was separately inserted into the single-guide RNA

2
expression DNA plasmids that contained the U6 promoter or the 7Sk promoter and the

guide RNA backbone DNA sequence. Lastly, the two DNA libraries were cut by the

typeIIS restriction endonuclease to release the specific overhang, allowing ordered

ligation to form the final DNA library. Compared with the CombiGEM method 1, this

strategy requires only two construction steps, is more flexible and has decreased

repetitive sequence.

S1.4 Gene selection, design and synthesis of sgRNAs

We first used the CIPHER method, which can systematically quantify the

concordance between diseases and genes and prioritize candidate genes for diseases,

to predict the top 100 candidate genes for INFLAMMATORY BOWEL DISEASE 1

(IBD1; OMIM ID 266600) and COLORECTAL CANCER (CRC; OMIM ID 114500),

respectively. We then selected 59 candidate genes, including a portion of the CIPHER-

related genes and a selection of genes in the following 12 manually summarized

KEGG pathways linking inflammation to cancer: (1) Inflammatory bowel disease (IBD);

(2) RAS signaling pathway; (3) Toll-like receptor signaling pathway; (4) NF-kappa B

signaling pathway; (5) JAK-STAT signaling pathway; (6) HIF-1 signaling pathway; (7)

PPAR signaling pathway; (8) MAPK signaling pathway; (9) TGF-beta signaling

pathway; (10) mTOR signaling pathway; (11) TNF signaling pathway; (12) PI3K-Akt

signaling pathway. In parallel, we selected 30 candidate genes for which we had

manually summarized linking inflammation to cancer. To find the differentially

expressed genes among the candidate genes, we employed a gene expression

dataset (GEO accession GSE4183) from the Gene Expression Omnibus (GEO) that

shows statistically significant differences in gene expression between IBD and normal

tissue and between CRC and normal tissue. This process selected 38 significant

differentially expressed genes (P-value < 0.05) linking inflammation to cancer. We then

removed the duplicated genes, finally selecting 84 candidate genes that are essential

in linking inflammation to cancer (Table S8).

3
 Next, we designed 3 sgRNAs targeting each gene and 20 negative control

sgRNAs that did not target sites in the human genome using the CRISPR-Era sgRNA

design tool (Table S4).

S1.5 Lentivirus packaging and infection

Foreign genes were stably integrated into the genome of the NCM460-Cas9 cell

line using third-generation lentiviral systems according to the protocol described below.

Genomic DNA Extraction, HiSeq 2500 Library Construction, Sequencing and

Sequence Analysis: To prepare samples from cultured cells for barcode sequencing,

genomic DNA was extracted using the TIANamp Genomic DNA Kit (TIANGEN Biotech,

Beijing). The primers used for PCR are listed in Table S5.

S1.6 Verification by RNA interference

We further used RNA interference to confirm the screening-based phenotypes.

Lentiviral vectors encoding an shRNA targeting a specific gene obtained from the

Tsinghua University shRNA library platform (http://center.biomed.tsinghua.edu.cn)

was purchased from Sigma-Aldrich. The TRC2-pLKO-puro vector used in this study

permits for transient or stable transfection of the shRNA as well as production of

lentiviral particles 2. Including the shRNA insert, the length of the TRC2-pLKO-puro

plasmid is 7,518 bp, as indicated in the vector map below (Fig. S3). The TRC2-pLKO-

puro vector lacking the shRNA insert has a length of 7,484 bp and the sequence listed

in Table S6.

At least three shRNAs vectors were selected for each gene and used to infect the

NCM460 cell line after lentiviral packaging. Finally, RNA was extracted abd used in

quantitative RT-PCR to verify the shRNA knockdown efficiency (Fig. S4). The shRNAs

that met certain knockdown efficiency criteria are listed in Table S7. The shRNAs were

then synthesized and used to construct lentiviral vectors that expressed a specific

fluorescent protein and resistance (Table S5).The vector construction service was

provided by Syngen Tech Co., LTD (Beijing).

4
S2 Computational methods
S2.1 Determination of sgRNA Phenotypes from Pooled Screens 3, 4
U
During exponential growth, the number of WT cells under normal condition, NWT ,

will increase over time as:

U
NWT (t )  NWT
U
(t 0 )  2gWT t

where gWT is the growth rate of WT cells under normal condition. We define the

effect of sgRNA X on N UX under normal condition, the growth of cells expressing X,

as  X , such that

N UX (t )  N UX (t 0 )  2(1 X )gWT t

 X can be calculated from the change in frequency of cells expressing X

compared with WT cells under normal condition as quantified by deep sequencing:

1 N UX (t ) / NWT
U
(t )
X  log 2
gWT t N X (t 0 ) / NWT (t 0 )
U U

For screens carried out in the presence of promotion by TGF  1, we define a

promotion kWT such that:

T
NWT (t )  NWT
T
(t 0 )  2( gWT  kWT )t

Then, we define the promotion that an sgRNA X confers to the promotion as  X ,

such that

N TX (t )  N TX (t 0 )  2[(1 X ) gWT  (1  X ) kWT ]t

To determine  X , frequencies of cells expressing sgRNAs are compared in

normal (U) and TGF  1 (T) populations:

1 N TX (t ) / NWT
T
(t )
X  log 2
kWT t N X (t ) / NWT (t )
U U

5
 Frequencies at t0 need not be measured to calculate  X as long as the normal

and TGF  1 populations are separated from a common parent population at t0 .

However, k needs to be calculated as the increase in growth rate that WT cells

experience under TGF  1 condition compared with normal condition. The promotion,

kWT , is calculated by measuring bulk population growth and monitoring the fraction of

mCherry-negative cells for both the normal and TGF  1 populations.

S2.2 Definitions for Expected Double-sgRNA Phenotypes 3,4

For sgRNAs X and Y with individual phenotypes  X and Y , the expected

phenotype for the double-sgRNA XY is  X  Y according to the sum definition and

is (1   X )  (1  Y )  1 according to the product definition. To derive the expected

double-shRNA phenotype from a linear fit, all single-sgRNA phenotypes were plotted

against the phenotypes of the same sgRNAs paired with X, and fit by linear regression.

We forced the linear function fX to assume  X for a single-shRNA phenotype of 0

(WT). Thus, the only degree of freedom for each bait was the slope of the linear fit.

Similarly, we fit a linear function fY describing the relationship between all single-

shRNA phenotypes and the phenotypes of the same sgRNAs paired with Y. fX ( Y )

and fY (  X ) generally agreed well, and we defined the fit-based expected double-

shRNA phenotype as the average of fX ( Y ) and fY (  X ) .

S2.3 Synergistic Module-based Drug Prediction

K  i      j  dGI  i , j  DS  k    K  i  S  i , k 
j i

where dGI  i , j  is the differential genetic interaction score of gene i and j ,

  j  is individual phenotype values of gene j , S  i , k  is the drugCIPHER score

of compound k . Given compound k , we can obtain the drug score ( DS ) for

6
differential genetic interaction of inflammation-induced cancer.

We ranked the compounds from analogous prescriptions of Liu-wei-di-huang

(LWDH), a classic herbal formula that have potential activities to inhibit inflammation-

induced tumorigenesis 5, according to their prediction scores and selected four

compounds as examples from four rank intervals (isorhamnetin, kaempferol,

quercetin and albiflorin). Consequently, we conducted an experimental validation of

these predictions. The outputs and the results of the cell viability assay are presented

in Table S11.

7
S3 Supplementary Figures

Fig.S1 Gene co-expression network analysis of microarray data. Pairwise

correlation is determined for each possible gene pair in the expression data.

8
 Fig.S2 Hierarchical assembly.

Fig.S3 TRC2 Vector Map (TRC2-pLKO-puro).

1.2

1
mRNA relative expression

0.8

0.6

0.4

0.2

Fig.S4 The knockdown efficiency of shRNAs.

9
 S4 Supplementary Tables
Table S1. DNA duplex
GTTCATCTCAACGGTAATCG
GGCGATTCGGCGACCTTAGT
GGCGCGAGTACGAAATTAAT
GGTTATATTGACGTCCTGCC
GCGCGGCTAGAATAGACTTG
GACTACGGACACCGCGACTC
GGTTCGTGCGGTAGTGTGCG
GGGCTGAACGCGTATTCGCG
GTATCGTCTTCCGTCCTCGT
GGCTACTCTATGCGTCGATT
GCTTAACAAAGCGAGCGACC
GATTATCAGACGCGCTGCGT
GGCACTGGACGATATCCGAC
GCGACCGAGGTGAAACGGCA
GCGCTCGATTTGCGCGAAAT
GACCAATTCAGCATCGGTGC
GCGAGCATATCTCTGCGCCC
GTACGCTACGGAGACGCAAA
GACTCACTCTTGACGAGTTA
GACTCGGGTTGGTGTTTCGC

Table S2. The plasmids sequences

Name Sequence
CTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTG
AGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAG
TCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTC
CCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCC
GACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATACGCGTACCGCT
AGCCAGGAAGAGTTTGTAGAAACGCAAAAAGGCCATCCGTCAGGATGG
pDC0 CCTTCTGCTTAGTTTGATGCCTGGCAGTTTATGGCGGGCGTCCTGCCCG
02 CCACCCTCCGGGCCGTTGCTTCACAACGTTCAAATCCGCTCCCGGCGG
ATTTGTCCTACTCAGGAGAGCGTTCACCGACAAACAACAGATAAAACGA
AAGGCCCAGTCTTCCGACTGAGCCTTTCGTTTTATTTGATGCCTGGCAG
TTCCCTACTCTCGCGTTAACGCTAGCATGGATGTTTTCCCAGTCACGAC
GTTGTAAAACGACGGCCAGTCTTAAGCTCGGGCCCGAGTTAACGCTACC
ATGGAGCTCCAAATAATGATTTTATTTTGACTGATAGTGACCTGTTCGTT
GCAACAAATTGATAAGCAATGCTTTTTTATAATGCCAACTTTGTATAGAAA
10
AGTTGGCTCCGAATTTCTCGAGGAATTCCAATTGACCATGACCGGTTTG
TCGAGCGTCTCACTGGTAGGACTCACATATGCTGCAGTATTTAGCATGC
CCCACCCATCTGCAAGGCATTCTGGATAGTGTCAAAACAGCCGGAAATC
AAGTCCGTTTATCTCAAACTTTAGCATTTTGGGAATAAATGATATTTGCTA
TGCTGGTTAAATTAGATTTTAGTTAAATTTCCTGCTGAAGCTCTAGTACG
ATAAGTAACTTGACCTAAGTGTAAAGTTGAGATTTCCTTCAGGTTTATATA
GCTTGTGCGCCGCCTGGGTACACCGTGAGACCGGATCCGCGCAACGCA
ATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTAT
GCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCAC
ACAGGAAACAGCTATGACCATGATTACGCCAAGCGCGCAATTAACCCTC
ACTAAAGGGAACAAAAGCTGGAGGACCTCGAGGGGGGGCCCGGTACC
CAATTCGCCCTATAGTGAGTCGTATTACGCGCGCTCACTGGCCGTCGTT
TTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCC
TTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCC
GCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGT
AAGTCGACGGTCTCAGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGG
CTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTTTTTA
AAGAATTCTCGACCTCGAGACAAATGCAGTACCGTATTACCGCCATGCA
TTAGTTATTAATGCTGAGACGACTAGTTAGGGCCCGGCGCCGCCTACGT
ACCCCGGGTAACTGATCATAATTCGACCCAAGTTTGTACAAAAAAGTTGA
ACGAGAAACGTAAAATGATATAAATATCAATATATTAAATTAGATTTTGCA
TAAAAAACAGACTACATAATACTGTAAAACACAACATATGCAGTCACTAT
GAACCAACTACTTAGATGGTATTAGTGACCTGTAGAATTAATTCGAGCTC
TAGAGCTGCAGGGCGGCCGCGATATCCCCTATAGTGAGTCGTATTACAT
GGTCATAGCTGTTTCCTGGCAGCTCTGGCCCGTGTCTCAAAATCTCTGA
TGTTACATTGCACAAGATAAAAATATATCATCATGAACAATAAAACTGTCT
GCTTACATAAACAGTAATACAAGGGGTGTTATGAGCCATATTCAACGGG
AAACGTCGAGGCCGCGATTAAATTCCAACATGGATGCTGATTTATATGG
GTATAAATGGGCTCGCGATAATGTCGGGCAATCAGGTGCGACAATCTAT
CGCTTGTATGGGAAGCCCGATGCGCCAGAGTTGTTTCTGAAACATGGCA
AAGGTAGCGTTGCCAATGATGTTACAGATGAGATGGTCAGACTAAACTG
GCTGACGGAATTTATGCCTCTTCCGACCATCAAGCATTTTATCCGTACTC
CTGATGATGCATGGTTACTCACCACTGCGATCCCCGGAAAAACAGCATT
CCAGGTATTAGAAGAATATCCTGATTCAGGTGAAAATATTGTTGATGCGC
TGGCAGTGTTCCTGCGCCGGTTGCATTCGATTCCTGTTTGTAATTGTCCT
TTTAACAGCGATCGCGTATTTCGTCTCGCTCAGGCGCAATCACGAATGA
ATAACGGTTTGGTTGATGCGAGTGATTTTGATGACGAGCGTAATGGCTG
GCCTGTTGAACAAGTCTGGAAAGAAATGCATAAACTTTTGCCATTCTCAC
CGGATTCAGTCGTCACTCATGGTGATTTCTCACTTGATAACCTTATTTTT
GACGAGGGGAAATTAATAGGTTGTATTGATGTTGGACGAGTCGGAATCG
CAGACCGATACCAGGATCTTGCCATCCTATGGAACTGCCTCGGTGAGTT
TTCTCCTTCATTACAGAAACGGCTTTTTCAAAAATATGGTATTGATAATCC

11
 TGATATGAATAAATTGCAGTTTCATTTGATGCTCGATGAGTTTTTCTAATC
AGAATTGGTTAATTGGTTGTAACACTGGCAGAGCATTACGCTGACTTGA
CGGGACGGCGCAAGCTCATGACCAAAATCCCTTAACGTGAGTTACGCG
TCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTT
GAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCA
CCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTT
TTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTTCT
TCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCG
CCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTG
GCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGA
TAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCA
GCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGC
TATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATC
CGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCA
GGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCT
GACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTAT
GGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTG
GCCTTTTGCTCACATGTT
CAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGG
AAGAGCAAAACAAAAGTAAGACCACCGCACAGCAAGCGGCCGCTGATC
TTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTAT
ATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAG
GCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGA
GCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCA
GCGTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAG
TGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCT
GTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCT
GGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGG
TTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTT
pDC0 GGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGA
05 GTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTG
AAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTA
GATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTG
GTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAA
TAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCA
CCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGG
CCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCC
ATTCGATTAGTGAACGGATCGGCACTGCGTGCGCCAATTCTGCAGACAA
ATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGT
ACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAAC
TAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTA
CAGGGACAGCAGAGATCCAGTTTGGTTAATTAACAACTTTGTATAGAAAA

12
GTTGGCTCCGAATTTCTCGACGTCGTGAGACGGGATCCGCGCAACGCA
ATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTAT
GCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCAC
ACAGGAAACAGCTATGACCATGATTACGCCAAGCGCGCAATTAACCCTC
ACTAAAGGGAACAAAAGCTGGAGGACCTCGAGGGGGGGCCCGGTACC
CAATTCGCCCTATAGTGAGTCGTATTACGCGCGCTCACTGGCCGTCGTT
TTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCC
TTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCC
GCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGT
AAGTCGACCGTCTCAATGCAATTCGCCCTTATTAATTGGCTCCGGTGCC
CGTCAGTGGGCAGAGCGCACATCGCCCACAGTCCCCGAGAAGTTGTGG
GGAGGGGTCGGCAATTGAACCGGTGCCTAGAGAAGGTGGCGCGGGGT
AAACTGGGAAAGTGATGTCGTGTACTGGCTCCGCCTTTTTCCCGAGGGT
GGGGGAGAACCGTATATAAGTGCAGTAGTCGCCGTGAACGTTCTTTTTC
GCAACGGGTTTGCCGCCAGAACACAGGTAAGTGCCGTGTGTGGTTCCC
GCGGGCCTGGCCTCTTTACGGGTTATGGCCCTTGCGTGCCTTGAATTAC
TTCCACCTGGCTGCAGTACGTGATTCTTGATCCCGAGCTTCGGGTTGGA
AGTGGGTGGGAGAGTTCGAGGCCTTGCGCTTAAGGAGCCCCTTCGCCT
CGTGCTTGAGTTGAGGCCTGGCCTGGGCGCTGGGGCCGCCGCGTGCG
AATCTGGTGGCACCTTCGCGCCTGTCTCGCTGCTTTCGATAAGTCTCTA
GCCATTTAAAATTTTTGATGACCTGCTGCGACGCTTTTTTTCTGGCAAGA
TAGTCTTGTAAATGCGGGCCAAGATCTGCACACTGGTATTTCGGTTTTTG
GGGCCGCGGGCGGCGACGGGGCCCGTGCGTCCCAGCGCACATGTTCG
GCGAGGCGGGGCCTGCGAGCGCGGCCACCGAGAATCGGACGGGGGT
AGTCTCAAGCTGGCCGGCCTGCTCTGGTGCCTGGCCTCGCGCCGCCGT
GTATCGCCCCGCCCTGGGCGGCAAGGCTGGCCCGGTCGGCACCAGTT
GCGTGAGCGGAAAGATGGCCGCTTCCCGGCCCTGCTGCAGGGAGCTC
AAAATGGAGGACGCGGCGCTCGGGAGAGCGGGCGGGTGAGTCACCCA
CACAAAGGAAAAGGGCCTTTCCGTCCTCAGCCGTCGCTTCATGTGACTC
CACGGAGTACCGGGCGCCGTCCAGGCACCTCGATTAGTTCTCGAGCTT
TTGGAGTACGTCGTCTTTAGGTTGGGGGGAGGGGTTTTATGCGATGGA
GTTTCCCCACACTGAGTGGGTGGAGACTGAAGTTAGGCCAGCTTGGCA
CTTGATGTAATTCTCCTTGGAATTTGCCCTTTTTGAGTTTGGATCTTGGTT
CATTCTCAAGCCTCAGACAGTGGTTCAAAGTTTTTTTCTTCCATTTCAGG
TCTAGTTAAGGGCCCGGCGCGCCTAAGGTACCCCCGGGTAACTGATCA
TAATTCGACCCAAGTTTGTACAAAAAAGCAGGCTGATTACCGGTCGCCA
CCATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATC
CTGGTCGAGCTGGACGGCGACGTAAACGGCCACAAGTTCAGCGTGTCC
GGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTT
CATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGAC
CACCTTCGGCTACGGCCTGCAGTGCTTCGCCCGCTACCCCGACCACAT
GAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCA

13
GGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGC
CGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAA
GGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGA
GTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAG
AACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGC
AGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCCATCGGCGAC
GGCCCCGTGCTGCTGCCCGACAACCACTACCTGAGCTACCAGTCCAAG
CTGAGCAAAGACCCCAACGAGAAGCGCGATCACATGGTCCTGCTGGAG
TTCGTGACCGCCGCCGGGATCACTCTCGGCATGGACGAGCTGTACAAG
GGATCTGGCGCCACCAACTTCTCTCTGCTGAAGCAGGCCGGCGACGTG
GAGGAGAACCCAGGCCCAGCTAGCATGACCGAGTACAAGCCCACGGTG
CGCCTCGCCACCCGCGACGACGTCCCCCGGGCCGTACGCACCCTCGC
CGCCGCGTTCGCCGACTACCCCGCCACGCGCCACACCGTCGACCCGG
ACCGCCACATCGAGCGGGTCACCGAGCTGCAAGAACTCTTCCTCACGC
GCGTCGGGCTCGACATCGGCAAGGTGTGGGTCGCGGACGACGGCGCC
GCGGTGGCGGTCTGGACCACGCCGGAGAGCGTCGAAGCGGGGGCGG
TGTTCGCCGAGATCGGCCCGCGCATGGCCGAGTTGAGCGGTTCCCGG
CTGGCCGCGCAGCAACAGATGGAAGGCCTCCTGGCGCCGCACCGGCC
CAAGGAGCCCGCGTGGTTCCTGGCCACCGTCGGCGTGTCGCCCGACC
ACCAGGGCAAGGGTCTGGGCAGCGCCGTCGTGCTCCCCGGAGTGGAG
GCGGCCGAGCGCGCCGGGGTGCCCGCCTTCCTGGAAACCTCCGCGCC
CCGCAACCTCCCCTTCTACGAGCGGCTCGGCTTCACCGTCACCGCCGA
CGTCGAGGTGCCCGAAGGACCGCGCACCTGGTGCATGACCCGCAAGC
CCGGTGCCTGAGCGGCCGCTATCGATCGTTTGATCCTAGATAACTGATC
TACCCAGCTTTCTTGTACAAAGTGGTGAATTCCGGCAATTCGATATCAAG
CTTATCGATAATCAACCTCTGGATTACAAAATTTGTGAAAGATTGACTGG
TATTCTTAACTATGTTGCTCCTTTTACGCTATGTGGATACGCTGCTTTAAT
GCCTTTGTATCATGCTATTGCTTCCCGTATGGCTTTCATTTTCTCCTCCTT
GTATAAATCCTGGTTGCTGTCTCTTTATGAGGAGTTGTGGCCCGTTGTCA
GGCAACGTGGCGTGGTGTGCACTGTGTTTGCTGACGCAACCCCCACTG
GTTGGGGCATTGCCACCACCTGTCAGCTCCTTTCCGGGACTTTCGCTTT
CCCCCTCCCTATTGCCACGGCGGAACTCATCGCCGCCTGCCTTGCCCG
CTGCTGGACAGGGGCTCGGCTGTTGGGCACTGACAATTCCGTGGTGTT
GTCGGGGAAATCATCGTCCTTTCCTTGGCTGCTCGCCTGTGTTGCCACC
TGGATTCTGCGCGGGACGTCCTTCTGCTACGTCCCTTCGGCCCTCAATC
CAGCGGACCTTCCTTCCCGCGGCCTGCTGCCGGCTCTGCGGCCTCTTC
CGCGTCTTCGCCTTCGCCCTCAGACGAGTCGGATCTCCCTTTGGGCCG
CCTCCCCGCATCGATACCGTCGACCTCGAGTCCTAGAAAAACATGGAGC
AATCACAAGTAGCAATACAGCAGCTACCAATGCTGATTGTGCCTGGCTA
GAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTA
CCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTT
AAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAACGAAGACA

14
AGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATT
GGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTG
GATGGTGCTACAAGCTAGTACCAGTTGAGCAAGAGAAGGTAGAAGAAG
CCAATGAAGGAGAGAACACCCGCTTGTTACACCCTGTGAGCCTGCATG
GGATGGATGACCCGGAGAGAGAAGTATTAGAGTGGAGGTTTGACAGCC
GCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGACTGTACTGG
GTGTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTA
GGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAG
TAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAG
ACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGGGCCCGTTTAAACCCG
CTGATCAGCCTCGACTGTGCCTTCTAGTTGCCAGCCATCTGTTGTTTGC
CCCTCCCCCGTGCCTTCCTTGACCCTGGAAGGTGCCACTCCCACTGTC
CTTTCCTAATAAAATGAGGAAATTGCATCGCATTGTCTGAGTAGGTGTCA
TTCTATTCTGGGGGGTGGGGTGGGGCAGGACAGCAAGGGGGAGGATT
GGGAAGACAATAGCAGGCATGCTGGGGATGCGGTGGGCTCTATGGCTT
CTGAGGCGGAAAGAACCAGCTGGGGCTCTAGGGGGTATCCCCACGCG
CCCTGTAGCGGCGCATTAAGCGCGGCGGGTGTGGTGGTTACGCGCAG
CGTGACCGCTACACTTGCCAGCGCCCTAGCGCCCGCTCCTTTCGCTTTC
TTCCCTTCCTTTCTCGCCACGTTCGCCGGCTTTCCCCGTCAAGCTCTAA
ATCGGGGGCTCCCTTTAGGGTTCCGATTTAGTGCTTTACGGCACCTCGA
CCCCAAAAAACTTGATTAGGGTGATGGTTCACGTAGTGGGCCATCGCCC
TGATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTTAATAG
TGGACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCGGTCTATT
CTTTTGATTTATAAGGGATTTTGCCGATTTCGGCCTATTGGTTAAAAAAT
GAGCTGATTTAACAAAAATTTAACGCGAATTAATTCTGTGGAATGTGTGT
CAGTTAGGGTGTGGAAAGTCCCCAGGCTCCCCAGCAGGCAGAAGTATG
CAAAGCATGCATCTCAATTAGTCAGCAACCAGGTGTGGAAAGTCCCCAG
GCTCCCCAGCAGGCAGAAGTATGCAAAGCATGCATCTCAATTAGTCAGC
AACCATAGTCCCGCCCCTAACTCCGCCCATCCCGCCCCTAACTCCGCC
CAGTTCCGCCCATTCTCCGCCCCATGGCTGACTAATTTTTTTTATTTATG
CAGAGGCCGAGGCCGCCTCTGCCTCTGAGCTATTCCAGAAGTAGTGAG
GAGGCTTTTTTGGAGGCCTAGGCTTTTGCAAAAAGCTCCCGGGAGCTTG
TATATCCATTTTCGGATCTGATCAGCACGTGTTGACAATTAATCATCGGC
ATAGTATATCGGCATAGTATAATACGACAAGGTGAGGAACTAAACCATG
GCCAAGTTGACCAGTGCCGTTCCGGTGCTCACCGCGCGCGACGTCGCC
GGAGCGGTCGAGTTCTGGACCGACCGGCTCGGGTTCTCCCGGGACTTC
GTGGAGGACGACTTCGCCGGTGTGGTCCGGGACGACGTGACCCTGTTC
ATCAGCGCGGTCCAGGACCAGGTGGTGCCGGACAACACCCTGGCCTG
GGTGTGGGTGCGCGGCCTGGACGAGCTGTACGCCGAGTGGTCGGAGG
TCGTGTCCACGAACTTCCGGGACGCCTCCGGGCCGGCCATGACCGAGA
TCGGCGAGCAGCCGTGGGGGCGGGAGTTCGCCCTGCGCGACCCGGCC
GGCAACTGCGTGCACTTCGTGGCCGAGGAGCAGGACTGACACGTGCTA

15
CGAGATTTCGATTCCACCGCCGCCTTCTATGAAAGGTTGGGCTTCGGAA
TCGTTTTCCGGGACGCCGGCTGGATGATCCTCCAGCGCGGGGATCTCA
TGCTGGAGTTCTTCGCCCACCCCAACTTGTTTATTGCAGCTTATAATGGT
TACAAATAAAGCAATAGCATCACAAATTTCACAAATAAAGCATTTTTTTCA
CTGCATTCTAGTTGTGGTTTGTCCAAACTCATCAATGTATCTTATCATGTC
TGTATACCGTCGACCTCTAGCTAGAGCTTGGCGTAATCATGGTCATAGC
TGTTTCCTGTGTGAAATTGTTATCCGCTCACAATTCCACACAACATACGA
GCCGGAAGCATAAAGTGTAAAGCCTGGGGTGCCTAATGAGTGAGCTAA
CTCACATTAATTGCGTTGCGCTCACTGCCCGCTTTCCAGTCGGGAAACC
TGTCGTGCCAGCTGCATTAATGAATCGGCCAACGCGCGGGGAGAGGCG
GTTTGCGTATTGGGCGCTCTTCCGCTTCCTCGCTCACTGACTCGCTGCG
CTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAAAGGCGGT
AATACGGTTATCCACAGAATCAGGGGATAACGCAGGAAAGAACATGTGA
GCAAAAGGCCAGCAAAAGGCCAGGAACCGTAAAAAGGCCGCGTTGCTG
GCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGAC
GCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGG
CGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCC
GCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTT
TCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCT
CCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCG
CCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTT
ATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTA
TGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTAC
ACTAGAAGAACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTT
CGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGT
AGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAG
GATCTCAAGAAGATCCTTTGATCTTTTCTACGGGGTCTGACGCTCAGTG
GAACGAAAACTCACGTTAAGGGATTTTGGTCATGACCAGCCAGGACAGA
AATGCCTCGACTTCGCTGCTACCCAAGGTTGCCGGGTGACGCACACCG
TGGAAACGGATGAAGGCACGAACCCAGTGGACATAAGCCTGTTCGGTT
CGTAAGCTGTAATGCAAGTAGCGTATGCGCTCACGCAACTGGTCCAGAA
CCTTGACCGAACGCAGCGGTGGTAACGGCGCAGTGGCGGTTTTCATGG
CTTGTTATGACTGTTTTTTTGGGGTACAGTCTATGCCTCGGGCATCCAAG
CAGCAAGCGCGTTACGCCGTGGGTCGATGTTTGATGTTATGGAGCAGC
AACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAAACATTA
TGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAG
TTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTT
GTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGTGATATTGA
TTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCT
TTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGA
TTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCC
GTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCG

16
CAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGAT
CTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAG
GTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATT
TGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTG
GGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTAC
AGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGG
GCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCT
AGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCA
GATCAGTTGGAAGAATTTGTCCACTACGTGAAAGGCGAGATCACCAAGG
TAGTCGGCAAATAATCATGAGCGGATACATATTTGAATGTATTTAGAAAA
ATAAACAAATAGGGGTTCCGCGCACATTTCCCCGAAAAGTGCCACCTGA
CGTCGACGGATCGGGAGATCTCCCGATCCCCTATGGTGCACTCTCAGT
ACAATCTGCTCTGATGCCGCATAGTTAAGCCAGTATCTGCTCCCTGCTT
GTGTGTTGGAGGTCGCTGAGTAGTGCGCGAGCAAAATTTAAGCTACAAC
AAGGCAAGGCTTGACCGACAATTGCATGAAGAATCTGCTTAGGGTTAGG
CGTTTTGCGCTGCTTCGCGATGTACGGGCCAGATATACGCGTTGACATT
GATTATTGACTAGTTATTAATAGTAATCAATTACGGGGTCATTAGTTCATA
GCCCATATATGGAGTTCCGCGTTACATAACTTACGGTAAATGGCCCGCC
TGGCTGACCGCCCAACGACCCCCGCCCATTGACGTCAATAATGACGTAT
GTTCCCATAGTAACGCCAATAGGGACTTTCCATTGACGTCAATGGGTGG
AGTATTTACGGTAAACTGCCCACTTGGCAGTACATCAAGTGTATCATATG
CCAAGTACGCCCCCTATTGACGTCAATGACGGTAAATGGCCCGCCTGG
CATTATGCCCAGTACATGACCTTATGGGACTTTCCTACTTGGCAGTACAT
CTACGTATTAGTCATCGCTATTACCATGGTGATGCGGTTTTGGCAGTACA
TCAATGGGCGTGGATAGCGGTTTGACTCACGGGGATTTCCAAGTCTCCA
CCCCATTGACGTCAATGGGAGTTTGTTTTGGCACCAAAATCAACGGGAC
TTTCCAAAATGTCGTAACAACTCCGCCCCATTGACGCAAATGGGCGGTA
GGCGTGTACGGTGGGAGGTCTATATAAGCAGCGCGTTTTGCCTGTACT
GGGTGTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAA
CTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTC
AAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCT
CAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACA
GGGACTTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGA
CTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTG
GTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGAT
GGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGCGATGG
GAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACA
TATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGC
CTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAAC
CATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTA
GCAACCCTCTATTGTGTGCAT

17
 CTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTG
AGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAG
TCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTC
CCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCC
GACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATACGCGTACCGCT
AGCCAGGAAGAGTTTGTAGAAACGCAAAAAGGCCATCCGTCAGGATGG
CCTTCTGCTTAGTTTGATGCCTGGCAGTTTATGGCGGGCGTCCTGCCCG
CCACCCTCCGGGCCGTTGCTTCACAACGTTCAAATCCGCTCCCGGCGG
ATTTGTCCTACTCAGGAGAGCGTTCACCGACAAACAACAGATAAAACGA
AAGGCCCAGTCTTCCGACTGAGCCTTTCGTTTTATTTGATGCCTGGCAG
TTCCCTACTCTCGCGTTAACGCTAGCATGGATGTTTTCCCAGTCACGAC
GTTGTAAAACGACGGCCAGTCTTAAGCTCGGGCCCGAGTTAACGCTACC
ATGGAGCTCCAAATAATGATTTTATTTTGACTGATAGTGACCTGTTCGTT
GCAACAAATTGATAAGCAATGCTTTTTTATAATGCCAACTTTGTATAGAAA
AGTTGGCTCCGAATTTCTCGAGGAATTCCAATTGACCATGACCGGTTTG
TCGAGCGTCTCAGTCGACAAGCTTCCCTTCACCGAGGGCCTATTTCCCA
TGATTCCTTCATATTTGCATATACGATACAAGGCTGTTAGAGAGATAATT
GGAATTAATTTGACTGTAAACACAAAGATATTAGTACAAAATACGTGACG
TAGAAAGTAATAATTTCTTGGGTAGTTTGCAGTTTTAAAATTATGTTTTAA
AATGGACTATCATATGCTTACCGTAACTTGAAAGTATTTCGATTTCTTGG
pDC0 CTTTATATATCTTGTGGAAAGGACGAAACACCGTGAGACCGGATCCGCG
07 CAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTA
CACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAAC
AATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCGCGCAAT
TAACCCTCACTAAAGGGAACAAAAGCTGGAGGACCTCGAGGGGGGGCC
CGGTACCCAATTCGCCCTATAGTGAGTCGTATTACGCGCGCTCACTGGC
CGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTT
AATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAG
AGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCG
AATGGTAAGTCGACGGTCTCAGTTTTAGAGCTAGAAATAGCAAGTTAAAA
TAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCTT
TTTTACTGGTGAGACGACTAGTTAAGGGCCCGGCGCGCCTAAGGTACC
CCCGGGTAACTGATCATAATTCGACCCAAGTTTGTACAAAAAAGTTGAAC
GAGAAACGTAAAATGATATAAATATCAATATATTAAATTAGATTTTGCATA
AAAAACAGACTACATAATACTGTAAAACACAACATATGCAGTCACTATGA
ACCAACTACTTAGATGGTATTAGTGACCTGTAGAATTAATTCGAGCTCTA
GAGCTGCAGGGCGGCCGCGATATCCCCTATAGTGAGTCGTATTACATG
GTCATAGCTGTTTCCTGGCAGCTCTGGCCCGTGTCTCAAAATCTCTGAT
GTTACATTGCACAAGATAAAAATATATCATCATGAACAATAAAACTGTCTG
CTTACATAAACAGTAATACAAGGGGTGTTATGAGCCATATTCAACGGGAA
ACGTCGAGGCCGCGATTAAATTCCAACATGGATGCTGATTTATATGGGT
ATAAATGGGCTCGCGATAATGTCGGGCAATCAGGTGCGACAATCTATCG

18
 CTTGTATGGGAAGCCCGATGCGCCAGAGTTGTTTCTGAAACATGGCAAA
GGTAGCGTTGCCAATGATGTTACAGATGAGATGGTCAGACTAAACTGGC
TGACGGAATTTATGCCTCTTCCGACCATCAAGCATTTTATCCGTACTCCT
GATGATGCATGGTTACTCACCACTGCGATCCCCGGAAAAACAGCATTCC
AGGTATTAGAAGAATATCCTGATTCAGGTGAAAATATTGTTGATGCGCTG
GCAGTGTTCCTGCGCCGGTTGCATTCGATTCCTGTTTGTAATTGTCCTTT
TAACAGCGATCGCGTATTTCGTCTCGCTCAGGCGCAATCACGAATGAAT
AACGGTTTGGTTGATGCGAGTGATTTTGATGACGAGCGTAATGGCTGGC
CTGTTGAACAAGTCTGGAAAGAAATGCATAAACTTTTGCCATTCTCACCG
GATTCAGTCGTCACTCATGGTGATTTCTCACTTGATAACCTTATTTTTGAC
GAGGGGAAATTAATAGGTTGTATTGATGTTGGACGAGTCGGAATCGCAG
ACCGATACCAGGATCTTGCCATCCTATGGAACTGCCTCGGTGAGTTTTC
TCCTTCATTACAGAAACGGCTTTTTCAAAAATATGGTATTGATAATCCTGA
TATGAATAAATTGCAGTTTCATTTGATGCTCGATGAGTTTTTCTAATCAGA
ATTGGTTAATTGGTTGTAACACTGGCAGAGCATTACGCTGACTTGACGG
GACGGCGCAAGCTCATGACCAAAATCCCTTAACGTGAGTTACGCGTCGT
TCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGA
TCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGC
TACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCC
GAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTTCTTCTA
GTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTA
CATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGA
TAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAG
GCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTT
GGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATG
AGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGT
AAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGG
GAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACT
TGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAA
AAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCT
TTTGCTCACATGTT

Table S3. Primer sequences

ATCACGTGGACTATCATATGCTTA
p668.1
CCGTAACT Sub1_Sample1 forward Primer
CGATGTTGGACTATCATATGCTTA
p668.2
CCGTAACT Sub1_Sample2 forward Primer
TTAGGCTGGACTATCATATGCTTA
p668.3
CCGTAACT Sub1_Sample3 forward Primer
TGACCATGGACTATCATATGCTTA
p668.4
CCGTAACT Sub1_Sample4 forward Primer
19
 ACATGTTGGACTATCATATGCTTA
p668.5
CCGTAACT Sub2_Sample1 forward Primer
GCCAATTGGACTATCATATGCTTA
p668.6
CCGTAACT Sub2_Sample2 forward Primer
CAGATCTGGACTATCATATGCTTA
p668.7
CCGTAACT Sub2_Sample3 forward Primer
ACTTGATGGACTATCATATGCTTA
p668.8
CCGTAACT Sub2_Sample4 forward Primer
GATCAGTGGACTATCATATGCTTA
p668.9
CCGTAACT Sub3_Sample1 forward Primer
TAGCTTTGGACTATCATATGCTTA
p668.10
CCGTAACT Sub3_Sample2 forward Primer
GGCTAGTGGACTATCATATGCTTA
p668.11
CCGTAACT Sub3_Sample3 forward Primer
CTTGTATGGACTATCATATGCTTA
p668.12
CCGTAACT Sub3_Sample4 forward Primer
ATCACGGCACCGGAGCCAATTAAT
p669.1
AAGGG Reverse Primer

Table S4. Information of 84 selected genes and designed sgRNAs

Gene symbol Sub-library Sequence
8877_SPHK1_1 Sub1 ACGCTCTGGTGGTCATGTC
8809_IL18R1_1 Sub1 AGAATTACCCTTGACCCTT
8772_FADD_1 Sub1 AGTGCAGCAGCACCAGGAA
8720_MBTPS1_1 Sub1 AAACATCTGGGCGACAGAC
85480_TSLP_1 Sub1 ACCTGATTACATATATGAG
8503_PIK3R3_1 Sub1 TACAATACGGTGTGGAGTA
8313_AXIN2_1 Sub1 GAAGAGACAGGCATGGGTT
7428_VHL_1 Sub1 AGGCAGGCGTCGAAGAGTA
7186_TRAF2_1 Sub1 CGGAGGACGTTTCTGCAGG
7157_TP53_1 Sub1 CATCAAATCATCCATTGCT
7132_TNFRSF1A_1 Sub1 ACCAGTCCAATAACCCCTG
7124_TNF_1 Sub1 CTGATTAGAGAGAGGTCCC
695_BTK_1 Sub1 ATGCTCTCCAGAATCACTG
6776_STAT5A_1 Sub1 GCCGTACAGCACCTGCATC
6774_STAT3_1 Sub1 CTGCTGTAGCTGATTCCAT
6772_STAT1_1 Sub1 CAGCTTGACTCAAAATTCC
673_BRAF_1 Sub1 CTTGTAACTGCTGAGGTGT

20
 672_BRCA1_1 Sub1 TTTCTATCATCCAAAGTAT
6714_SRC_1 Sub1 AGAACGTGCACGGCGCTGG
6667_SP1_1 Sub1 CTGTGGTGAAAATTGAAAA
64127_NOD2_1 Sub1 AAAGAGCAAGTGTCCTCCT
5979_RET_1 Sub1 AAGAAGGAGAAGTATACGC
5971_RELB_1 Sub1 AACGGCTTCGGCCTGGACG
5970_RELA_1 Sub1 ACAAGTGGCCATTGTGTTC
5966_REL_1 Sub1 GCTACTATGAAGCAGAATT
595_CCND1_1 Sub1 TCGTTGAGGAGGTTGGCAT
5933_RBL1_1 Sub1 ATGGCAGTAAAGTCGTCCA
59067_IL21_1 Sub1 AGATCCAGTCCTGGCAACA
5899_RALB_1 Sub1 AAAGAAAGTGGTTCTTGAT
58985_IL22RA1_1 Sub1 CTGCTGACCATCTTGACTG
5891_MOK_1 Sub1 TTCATTTACTCCAGGAAAG
5743_PTGS2_1 Sub1 GGTACAATCGCACTTATAC
5601_MAPK9_1 Sub1 CTGAAACCAATTGGCTCTG
5371_PML_1 Sub1 AACTCCTCCTCCGAAGCGG
5295_PIK3R1_1 Sub1 AAGATATTGACTTGCACTT
5290_PIK3CA_1 Sub1 ACCATCATCAGGTGAACTG
51561_IL23A_1 Sub1 CTCTGCCCTGAGCTGTCCA
50616_IL22_1 Sub1 CTCACAGATTTCTGCAGGG
50615_IL21R_1 Sub1 GTAATCGGTGTAGCAGACG
4791_NFKB2_1 Sub1 ATCGTGGAACAGCCTAAGC
4790_NFKB1_1 Sub1 CTCTAATATTTGAAGGTAT
472_ATM_1 Sub1 ATGCAGGAAATCAGTAGTT
4609_MYC_1 Sub1 TTGGTGAAGCTAACGTTGA
4436_MSH2_1 Sub1 ACGCTGCAGTTGGAGAGCG
4296_MAP3K11_1 Sub1 CTGCCTTTGGAGACCCCTC
4170_MCL1_1 Sub1 GACTCAACCTCTACTGTGG
4088_SMAD3_1 Sub1 TTCGCCTTCAATATGAAGA
3932_LCK_1 Sub1 CTCACACCCGGAAGATGAC
3925_STMN1_1 Sub1 AACTGGAGAAGCGTGCCTC
3845_KRAS_1 Sub1 GACCAGTACATGAGGACTG
3726_JUNB_1 Sub1 TATGAGTCGTCGTGGTAGA
3717_JAK2_1 Sub1 CAAATAGATCCAGTTCTTC
3716_JAK1_1 Sub1 AGGAGCTCCAAGAAGACTG
367_AR_1 Sub1 GTGGAAAGTAATAGTCAAT
3661_IRF3_1 Sub1 AAGCGGCTGTTGGTGCCGG
21
 3594_IL12RB1_1 Sub1 AGTCTGCATCCGGATATGG
3588_IL10RB_1 Sub1 GTACTGAGCTGTGAAAGTC
3587_IL10RA_1 Sub1 CCAGCAGCACTACGAGGCA
3586_IL10_1 Sub1 TTGCCTGGTCCTCCTGACT
3570_IL6R_1 Sub1 TCAGAGTCACGCTGTCTCC
3569_IL6_1 Sub1 AATCTTCTCCTGGGGGTAC
3562_IL3_1 Sub1 AGTTGGAGCAGGAGCAGGA
3554_IL1R1_1 Sub1 AGGCTTGTTCTGTAGATAC
3551_IKBKB_1 Sub1 GGAAATGAAAGAGCGCCTT
3455_IFNAR2_1 Sub1 AGGTCACAAAATGATCTTG
3265_HRAS_1 Sub1 ACGGAATATAAGCTGGTGG
324_APC_1 Sub1 CAAGTTGAGGCACTGAAGA
3146_HMGB1_1 Sub1 CGACTCTGTGCCTCGCTGA
3091_HIF1A_1 Sub1 AACTCACATTATGTGGAAG
2956_MSH6_1 Sub1 GCGCTGAGTGATGCCAACA
29110_TBK1_1 Sub1 CTACTGCAAATGTCTTTCG
282618_IFNL1_1 Sub1 ACCGTGGTGCTGGTGACTT
282617_IFNL3_1 Sub1 CTCAGCCTCCAAAGCCACG
282616_IFNL2_1 Sub1 CTGGTCCAAGACGTCCACC
2264_FGFR4_1 Sub1 CCTCCAGTCTTGTCCCTGG
1901_S1PR1_1 Sub1 AACAGCATTAAACTGACCT
1874_E2F4_1 Sub1 TTCGTGTCCCTTCTGCAGG
1869_E2F1_1 Sub1 GAGATGATGACGATCTGCG
1630_DCC_1 Sub1 AATAGTCTTAGATGTGTTT
149233_IL23R_1 Sub1 AATCAGGTCACTATTCAAT
1487_CTBP1_1 Sub1 TCCGACCTCCGATCATGAA
1386_ATF2_1 Sub1 CAAGAGGGGATAAATCTAG
116379_IL22RA2_1 Sub1 ACTGAAATTGTACCCTCTG
1019_CDK4_1 Sub1 AAATTGGTGTCGGTGCCTA
8877_SPHK1_2 Sub2 AGTCACGTGCAGCCCCTTT
8809_IL18R1_2 Sub2 AGCAATGTTTCAGATAGAA
8772_FADD_2 Sub2 TTCCTGGTGCTGCTGCACT
8720_MBTPS1_2 Sub2 AATATATTGTGGCTTTCAA
85480_TSLP_2 Sub2 CCTTAGCTATCTGGTGCCC
8503_PIK3R3_2 Sub2 TCATTGGCTTAGGTGGCTT
8313_AXIN2_2 Sub2 TGTTGGAAGAGACAGGCAT
7428_VHL_2 Sub2 AGGGCGGAGAACTGGGACG
7186_TRAF2_2 Sub2 CTTCTCCAAGACCCTCCTG
22
 7157_TP53_2 Sub2 GATGATTTGATGCTGTCCC
7132_TNFRSF1A_2 Sub2 GTGGGAATATACCCCTCAG
7124_TNF_2 Sub2 GCTACAGGCTTGTCACTCG
695_BTK_2 Sub2 ATCACTTGTGTTGAAACAG
6776_STAT5A_2 Sub2 GACCTCGATGGGGAAGTGC
6774_STAT3_2 Sub2 CAGCTTGACACACGGTACC
6772_STAT1_2 Sub2 AAAACTGTCATCATAAAGC
673_BRAF_2 Sub2 TGAATATCCTACTCTTCAT
672_BRCA1_2 Sub2 GTTTCTGTAGCCCATACTT
6714_SRC_2 Sub2 AGCCCGCCGAGAACGTGCA
6667_SP1_2 Sub2 TGAAAATTGAAAAAGGAGT
64127_NOD2_2 Sub2 ACACTCTCGAAGCCTTCCA
5979_RET_2 Sub2 ACGTACAGCAAGGGCGTGC
5971_RELB_2 Sub2 ACGAGTACATCAAGGAGAA
5970_RELA_2 Sub2 AAGGCACAGCAATGCGTCG
5966_REL_2 Sub2 TTGGAAAAGACTGCAGAGA
595_CCND1_2 Sub2 GTCTCCTCCGCCTTCAGCA
5933_RBL1_2 Sub2 GATGGCAGTAAAGTCGTCC
59067_IL21_2 Sub2 AGGATTGTCATCTGTCTGA
5899_RALB_2 Sub2 AGATAACTACTTTCGGAGT
58985_IL22RA1_2 Sub2 CAGATCCGAGGGGTCCTCA
5891_MOK_2 Sub2 TACCAGTTATGTAAGTCCC
5743_PTGS2_2 Sub2 TAGTGCACTGTGTTTGGAG
5601_MAPK9_2 Sub2 CTGCATTTGATACAGTTCT
5371_PML_2 Sub2 GAACTCCTCCTCCGAAGCG
5295_PIK3R1_2 Sub2 ACATATTGACTGTGAATAA
5290_PIK3CA_2 Sub2 GATTCTTGGGGGCATCAAG
51561_IL23A_2 Sub2 CTGGCACTGAGTCCAGGCA
50616_IL22_2 Sub2 GCCAAGAGAAGGAGGCAGC
50615_IL21R_2 Sub2 ATGACCGTCTGGAGGTAAT
4791_NFKB2_2 Sub2 TTCCACGATCACCAGGTAG
4790_NFKB1_2 Sub2 CAGAAGATGATCCATATTT
472_ATM_2 Sub2 TGAAATATCTCAGCAACAG
4609_MYC_2 Sub2 TCGAGGTCATAGTTCCTGT
4436_MSH2_2 Sub2 AAGCGCACGAAGCCGACCT
4296_MAP3K11_2 Sub2 AGGGGTCTCCAAAGGCAGC
4170_MCL1_2 Sub2 ACTCAACCTCTACTGTGGG
4088_SMAD3_2 Sub2 TGTCTCTACTCTCTGGTAG
23
 3932_LCK_2 Sub2 CTCATCCGAAATGGCTCTG
3925_STMN1_2 Sub2 GAGGGGAAAGGGGGAATTC
3845_KRAS_2 Sub2 GGACCAGTACATGAGGACT
3726_JUNB_2 Sub2 ACGACTCATACACAGCTAC
3717_JAK2_2 Sub2 TGTATCTTTACCATTCCCT
3716_JAK1_2 Sub2 AAGACTGAGGTGAACCTGG
367_AR_2 Sub2 GGTGGAAAGTAATAGTCAA
3661_IRF3_2 Sub2 ACATTCTGGATGAGTTACT
3594_IL12RB1_2 Sub2 ATAGCATCTCAGGTCCCTA
3588_IL10RB_2 Sub2 TGACCACACCTTGAGAGTC
3587_IL10RA_2 Sub2 TGCCTCGTAGTGCTGCTGG
3586_IL10_2 Sub2 GTGCAGCTGTTCTCAGACT
3570_IL6R_2 Sub2 ATGGGCTGGCATGGGAAGG
3569_IL6_2 Sub2 GAGAAGGCAACTGGACCGA
3562_IL3_2 Sub2 TCATGGGAGCTTGGAGTCC
3554_IL1R1_2 Sub2 TTTGTTCCTGCTAAGGTGG
3551_IKBKB_2 Sub2 AAAGAGCGCCTTGGGACAG
3455_IFNAR2_2 Sub2 CCTATGTCACCGTCCTAGA
3265_HRAS_2 Sub2 GAATATAAGCTGGTGGTGG
324_APC_2 Sub2 AAGTACTTAAACAACTACA
3146_HMGB1_2 Sub2 TTACAGAGCGGAGAGAGTG
3091_HIF1A_2 Sub2 ATGGTAAGCCTCATCACAG
2956_MSH6_2 Sub2 AGTGATGCCAACAAGGCCT
29110_TBK1_2 Sub2 AAGAACCTTCTAATGCCTA
282618_IFNL1_2 Sub2 TGCTGGTGACTTTGGTGCT
282617_IFNL3_2 Sub2 CTGGGAGAGGATATGGTGC
282616_IFNL2_2 Sub2 CTCAGCCTCCAAAGCCATG
2264_FGFR4_2 Sub2 CCTCCAGGGACAAGACTGG
1901_S1PR1_2 Sub2 AATTCCATGCCGGCGATGA
1874_E2F4_2 Sub2 CCGCTTCTGGCGTACAGCT
1869_E2F1_2 Sub2 TGGCGAAGAGCAGCAGGTC
1630_DCC_2 Sub2 AAGAGTACAAAAGCCAGCT
149233_IL23R_2 Sub2 GCAGTTCTTAATTGCTGCT
1487_CTBP1_2 Sub2 CCCGTTCATGATCGGAGGT
1386_ATF2_2 Sub2 GTGAGGTAAAGGACTATCC
116379_IL22RA2_2 Sub2 CCAGCATCCACTTGGCTTC
1019_CDK4_2 Sub2 TGGCCACTGTGGGGATCAC
8877_SPHK1_3 Sub3 ATTTCAGCCTCAGCCAAAA
24
 8809_IL18R1_3 Sub3 TACAAAAGCAGTGGATCAC
8772_FADD_3 Sub3 AGGCATAGGAACTTGAGCT
8720_MBTPS1_3 Sub3 AATCACCTCAAAATCACTA
85480_TSLP_3 Sub3 CCTGGGCACCAGATAGCTA
8503_PIK3R3_3 Sub3 CTGAAGTCATTGGCTTAGG
8313_AXIN2_3 Sub3 GTGTTGGAAGAGACAGGCA
7428_VHL_3 Sub3 AGTACGGCCCTGAAGAAGA
7186_TRAF2_3 Sub3 TAGCAACTCCAGGGAGCCA
7157_TP53_3 Sub3 GCATTCTGGGAGCTTCATC
7132_TNFRSF1A_3 Sub3 TACAATGACTGTCCAGGCC
7124_TNF_3 Sub3 GGCTACAGGCTTGTCACTC
695_BTK_3 Sub3 GAATCTGTCTTTCTGGAGG
6776_STAT5A_3 Sub3 TGGCTTGGGCTCTGTCCTG
6774_STAT3_3 Sub3 AAACTGCCGCAGCTCCATT
6772_STAT1_3 Sub3 GTGGCAAATGAAACATCAT
673_BRAF_3 Sub3 AAGACCTCACAGTAAAAAT
672_BRCA1_3 Sub3 AACTCTGAGGACAAAGCAG
6714_SRC_3 Sub3 CCAGCGCCGTGCACGTTCT
6667_SP1_3 Sub3 GTGGCAATAATGGGGGCAA
64127_NOD2_3 Sub3 GACACTCTCGAAGCCTTCC
5979_RET_3 Sub3 ATGAGCGGGCCCTCACCAT
5971_RELB_3 Sub3 AGAACGGCTTCGGCCTGGA
5970_RELA_3 Sub3 ATCAGCCAGGCCTCGGCCT
5966_REL_3 Sub3 ATCAGCAGGCAGCATTCCA
595_CCND1_3 Sub3 CGACGATCTTCCGCATGGA
5933_RBL1_3 Sub3 ACGACTTTACTGCCATCCG
59067_IL21_3 Sub3 TCTGATGGTCATCTTCTTG
5899_RALB_3 Sub3 AGTAAGGGCCAGAGCTCCT
58985_IL22RA1_3 Sub3 ATGCTGTAGACCGTGTCTG
5891_MOK_3 Sub3 ATCCAGGGACTTACATAAC
5743_PTGS2_3 Sub3 GGCTCTAGTATAATAGGAG
5601_MAPK9_3 Sub3 AGTTTGGTTCTGAAAAGGA
5371_PML_3 Sub3 CAGACAAGGCAGCAGCTTC
5295_PIK3R1_3 Sub3 TAGCTCTTGGATTCAGTGA
5290_PIK3CA_3 Sub3 TAGAATGTTTACTACCAAA
51561_IL23A_3 Sub3 ATGTTCCCCATATCCAGTG
50616_IL22_3 Sub3 TACCAAGAGGGCCAAGAGA
50615_IL21R_3 Sub3 GATGCAGATGACCGTCTGG
25
 4791_NFKB2_3 Sub3 TTTCTGGGGCTGGCTCCTT
4790_NFKB1_3 Sub3 AAGCTGTCAGCGCGTCGCC
472_ATM_3 Sub3 GATGCTGTTCTCAGACTGA
4609_MYC_3 Sub3 CTGCACCGAGTCGTAGTCG
4436_MSH2_3 Sub3 GCTTCGTGCGCTTCTTTCA
4296_MAP3K11_3 Sub3 GCAGCGGGTTATGCCAACC
4170_MCL1_3 Sub3 AGTCTGGCGTGAGGGTGGA
4088_SMAD3_3 Sub3 TGTGGCGTGGCACCAACAC
3932_LCK_3 Sub3 ACCCACTGGTTACCTACGA
3925_STMN1_3 Sub3 CTTCAAGACCTCAGCTTCA
3845_KRAS_3 Sub3 ACTCAGTGGGAAAACTTCA
3726_JUNB_3 Sub3 TGTAGAGAGAGGCCACCAG
3717_JAK2_3 Sub3 ATTATCTGACCTTTCCATC
3716_JAK1_3 Sub3 GAAGTGATCTTCTATCTGT
367_AR_3 Sub3 AAGCTTCTGGGTGTCACTA
3661_IRF3_3 Sub3 AGTGGGATTGTCCAAGCTG
3594_IL12RB1_3 Sub3 GAGCACTCGTAACGATCAC
3588_IL10RB_3 Sub3 TACTTCTACTTGCATTCCA
3587_IL10RA_3 Sub3 AGCGTCTGAGCCAAGACGG
3586_IL10_3 Sub3 GGTGCAGCTGTTCTCAGAC
3570_IL6R_3 Sub3 CAAGTGCACAGTCCCAGCT
3569_IL6_3 Sub3 TCCAGTTGCCTTCTCCCTG
3562_IL3_3 Sub3 GTCATGGGAGCTTGGAGTC
3554_IL1R1_3 Sub3 GGTAGTTTCTGCTTAAATA
3551_IKBKB_3 Sub3 ATTTGGAAATGTCATCCGA
3455_IFNAR2_3 Sub3 ATACACAGTAGTTCGTGTT
3265_HRAS_3 Sub3 AATATAAGCTGGTGGTGGT
324_APC_3 Sub3 ATGAAGCTATGGCTTCTTC
3146_HMGB1_3 Sub3 AGAGTGAGGAGGCTGCGTC
3091_HIF1A_3 Sub3 TGAGGAAACTTCTGGATGC
2956_MSH6_3 Sub3 TAAACCAGACAAGGCCACC
29110_TBK1_3 Sub3 GTAGTCCATAGGCATTAGA
282618_IFNL1_3 Sub3 GTGACTTTGGTGCTAGGCT
282617_IFNL3_3 Sub3 CCTCCACCATTGGCTGCAC
282616_IFNL2_3 Sub3 CCTCCACCATTGGCTGTAC
2264_FGFR4_3 Sub3 AGGCCTCCAGGGACAAGAC
1901_S1PR1_3 Sub3 ACACAGGGTTGGCACCATG
1874_E2F4_3 Sub3 ATCGAGGAGCTGCAGCAGC
26
 1869_E2F1_3 Sub3 GAAACTGACCATCAGTACC
1630_DCC_3 Sub3 ATGCCGTCACAATGCGGGG
149233_IL23R_3 Sub3 GATTAATAAAACAACAGCT
1487_CTBP1_3 Sub3 CCATCCAGCAATGCCACCA
1386_ATF2_3 Sub3 TAGACTCTGGGTGAGGTAA
116379_IL22RA2_3 Sub3 GAAAAATAAAGAAGACTGT
1019_CDK4_3 Sub3 GGGACTCTCACACTCTTGA
0_0_9 NC TATCGTCTTCCGTCCTCGT
0_0_8 NC GGCTGAACGCGTATTCGCG
0_0_7 NC GTTCGTGCGGTAGTGTGCG
0_0_6 NC ACTACGGACACCGCGACTC
0_0_5 NC CGCGGCTAGAATAGACTTG
0_0_4 NC GTTATATTGACGTCCTGCC
0_0_3 NC GCGCGAGTACGAAATTAAT
0_0_20 NC ACTCGGGTTGGTGTTTCGC
0_0_2 NC GCGATTCGGCGACCTTAGT
0_0_19 NC ACTCACTCTTGACGAGTTA
0_0_18 NC TACGCTACGGAGACGCAAA
0_0_17 NC CGAGCATATCTCTGCGCCC
0_0_16 NC ACCAATTCAGCATCGGTGC
0_0_15 NC CGCTCGATTTGCGCGAAAT
0_0_14 NC CGACCGAGGTGAAACGGCA
0_0_13 NC GCACTGGACGATATCCGAC
0_0_12 NC ATTATCAGACGCGCTGCGT
0_0_11 NC CTTAACAAAGCGAGCGACC
0_0_10 NC GCTACTCTATGCGTCGATT
0_0_1 NC TTCATCTCAACGGTAATCG

Table S5. Primer sequences for quantitative RT-PCR

Gene Sequences (5’ to 3’)
Symbol Forward Reverse
L1CAM TCACGGGCAACAACAGCAACT CGGCTTCCTGTCAATCATGCT
Slug ATATTCGGACCCACACATTACCT GCAAATGCTCTGTTGCAGTGA
PTGS2 ACCAGAGCAGGCAGATGAAAT TACCAGAAGGGCAGGATACAG
ACTIN GTGGACATCCGCAAAGAC AAAGGGTGTAACGCAACTA
GAPDH AGCCACATCGCTCAGACAC GCCCAATACGACCAAATCC
TNF TGGCGTGGAGCTGAGAGATAA TTGATGGCAGAGAGGAGGTTGA

27
IL6R CCCCTCAGCAATGTTGTTTGT CCCCTCAGCAATGTTGTTTGT
CDK4 ATGGCTACCTCTCGATATGAGC CATTGGGGACTCTCACACTCT
MYC GGCTCCTGGCAAAAGGTCA CTGCGTAGTTGTGCTGATGT
NFKB1 AACAGAGAGGATTTCGTTTCCG TTTGACCTGAGGGTAAGACTTCT
PIK3CA CCACGACCATCATCAGGTGAA CCTCACGGAGGCATTCTAAAGT

Table S6. TRC2-pLKO-puro sequence (without shRNA insert, 7484bp)

> TRC2-pLKO-puro (direct) 7484bp

CCCGGGTTGCGCCTTTTCCAAGGCAGCCCTGGGTTTGCGCAGGGACGCGGCTGCTCTGGGCGTGGTTCCG

GGAAACGCAGCGGCGCCGACCCTGGGTCTCGCACATTCTTCACGTCCGTTCGCAGCGTCACCCGGATCTT

CGCCGCTACCCTTGTGGGCCCCCCGGCGACGCTTCCTGCTCCGCCCCTAAGTCGGGAAGGTTCCTTGCGG

TTCGCGGCGTGCCGGACGTGACAAACGGAAGCCGCACGTCTCACTAGTACCCTCGCAGACGGACAGCGCC

AGGGAGCAATGGCAGCGCGCCGACCGCGATGGGCTGTGGCCAATAGCGGCTGCTCAGCAGGGCGCGCCGA

GAGCAGCGGCCGGGAAGGGGCGGTGCGGGAGGCGGGGTGTGGGGCGGTAGTGTGGGCCCTGTTCCTGCCC

GCGCGGTGTTCCGCATTCTGCAAGCCTCCGGAGCGCACGTCGGCAGTCGGCTCCCTCGTTGACCGAATCA

CCGACCTCTCTCCCCAGGGGGATCCACCGGAGCTTACCATGACCGAGTACAAGCCCACGGTGCGCCTCGC

CACCCGCGACGACGTCCCCAGGGCCGTACGCACCCTCGCCGCCGCGTTCGCCGACTACCCCGCCACGCGC

CACACCGTCGATCCGGACCGCCACATCGAGCGGGTCACCGAGCTGCAAGAACTCTTCCTCACGCGCGTCG

GGCTCGACATCGGCAAGGTGTGGGTCGCGGACGACGGCGCCGCCGTGGCGGTCTGGACCACGCCGGAGAG

CGTCGAAGCGGGGGCGGTGTTCGCCGAGATCGGCCCGCGCATGGCCGAGTTGAGCGGTTCCCGGCTGGCC

GCGCAGCAACAGATGGAAGGCCTCCTGGCGCCGCACCGGCCCAAGGAGCCCGCGTGGTTCCTGGCCACCG

TCGGCGTCTCGCCCGACCACCAGGGCAAGGGTCTGGGCAGCGCCGTCGTGCTCCCCGGAGTGGAGGCGGC

CGAGCGCGCCGGGGTGCCCGCCTTCCTGGAGACCTCCGCGCCCCGCAACCTCCCCTTCTACGAGCGGCTC

GGCTTCACCGTCACCGCCGACGTCGAGGTGCCCGAAGGACCGCGCACCTGGTGCATGACCCGCAAGCCCG

GTGCCTGAACGCGTTAAGTCGACAATCAACCTCTGGATTACAAAATTTGTGAAAGATTGACTGGTATTCT

TAACTATGTTGCTCCTTTTACGCTATGTGGATACGCTGCTTTAATGCCTTTGTATCATGCTATTGCTTCC

CGTATGGCTTTCATTTTCTCCTCCTTGTATAAATCCTGGTTGCTGTCTCTTTATGAGGAGTTGTGGCCCG

TTGTCAGGCAACGTGGCGTGGTGTGCACTGTGTTTGCTGACGCAACCCCCACTGGTTGGGGCATTGCCAC

CACCTGTCAGCTCCTTTCCGGGACTTTCGCTTTCCCCCTCCCTATTGCCACGGCGGAACTCATCGCCGCC

TGCCTTGCCCGCTGCTGGACAGGGGCTCGGCTGTTGGGCACTGACAATTCCGTGGTGTTGTCGGGGAAAT

CATCGTCCTTTCCTTGGCTGCTCGCCTGTGTTGCCACCTGGATTCTGCGCGGGACGTCCTTCTGCTACGT

CCCTTCGGCCCTCAATCCAGCGGACCTTCCTTCCCGCGGCCTGCTGCCGGCTCTGCGGCCTCTTCCGCGT

CTTCGCCTTCGCCCTCAGACGAGTCGGATCTCCCTTTGGGCCGCCTCCCCGCGTCGACTTTAAGACCAAT

GACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCAC

TCCCAACGAAGACAAGATCTGCTTTTTGCTTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGG

AGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGT

GTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATC

TCTAGCAGTACGTATAGTAGTTCATGTCATCTTATTATTCAGTATTTATAACTTGCAAAGAAATGAATAT

CAGAGAGTGAGAGGAACTTGTTTATTGCAGCTTATAATGGTTACAAATAAAGCAATAGCATCACAAATTT

CACAAATAAAGCATTTTTTTCACTGCATTCTAGTTGTGGTTTGTCCAAACTCATCAATGTATCTTATCAT

GTCTGGCTCTAGCTATCCCGCCCCTAACTCCGCCCATCCCGCCCCTAACTCCGCCCAGTTCCGCCCATTC

TCCGCCCCATGGCTGACTAATTTTTTTTATTTATGCAGAGGCCGAGGCCGCCTCGGCCTCTGAGCTATTC

28
CAGAAGTAGTGAGGAGGCTTTTTTGGAGGCCTAGGGACGTACCCAATTCGCCCTATAGTGAGTCGTATTA

CGCGCGCTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGC

CTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAAC

AGTTGCGCAGCCTGAATGGCGAATGGGACGCGCCCTGTAGCGGCGCATTAAGCGCGGCGGGTGTGGTGGT

TACGCGCAGCGTGACCGCTACACTTGCCAGCGCCCTAGCGCCCGCTCCTTTCGCTTTCTTCCCTTCCTTT

CTCGCCACGTTCGCCGGCTTTCCCCGTCAAGCTCTAAATCGGGGGCTCCCTTTAGGGTTCCGATTTAGTG

CTTTACGGCACCTCGACCCCAAAAAACTTGATTAGGGTGATGGTTCACGTAGTGGGCCATCGCCCTGATA

GACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTTAATAGTGGACTCTTGTTCCAAACTGGAACA

ACACTCAACCCTATCTCGGTCTATTCTTTTGATTTATAAGGGATTTTGCCGATTTCGGCCTATTGGTTAA

AAAATGAGCTGATTTAACAAAAATTTAACGCGAATTTTAACAAAATATTAACGCTTACAATTTAGGTGGC

ACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGC

TCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGAGTATTCAACATTT

CCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTG

AAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTA

AGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGG

CGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGAC

TTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTG

CTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCT

AACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAA

GCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAA

CTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGG

ACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGG

TCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGG

GGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTG

GTAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGG

ATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAG

CGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTT

GCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCG

AAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTTCTTCTAGTGTAGCCGTAGTTAGGCCACC

ACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAG

TGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGC

TGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGC

GTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGT

CGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTT

CGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCA

GCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATC

CCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACC

GAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTT

GGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAAT

TAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGT

GGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCGCGCAATTA

ACCCTCACTAAAGGGAACAAAAGCTGGAGCTGCAAGCTTAATGTAGTCTTATGCAATACTCTTGTAGTCT

29
 TGCAACATGGTAACGATGAGTTAGCAACATGCCTTACAAGGAGAGAAAAAGCACCGTGCATGCCGATTGG

TGGAAGTAAGGTGGTACGATCGTGCCTTATTAGGAAGGCAACAGACGGGTCTGACATGGATTGGACGAAC

CACTGAATTGCCGCATTGCAGAGATATTGTATTTAAGTGCCTAGCTCGATACATAAACGGGTCTCTCTGG

TTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCT

TGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACC

CTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACTTGAAAGCGAAAGGGAAACCAG

AGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGT

GAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAG

CGGGGGAGAATTAGATCGCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAA

AACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGA

AGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTA

TATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAG

ACAAGATAGAGGAAGAGCAAAACAAAAGTAAGACCACCGCACAGCAAGCGGCCGCTGATCTTCAGACCTG

GAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATT

AGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCT

TTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCGTCAATGACGCTGACGGTACAGG

CCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCA

TCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTA

AAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGA

ATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGA

AATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAA

CAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGT

ATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTAT

AGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCC

AGAGAGGGCCTATTTCCCATGATTCCTTCATATTTGCATATACGATACAAGGCTGTTAGAGAGATAATTA

GAATTAATTTGACTGTAAACACAAAGATATTAGTACAAAATACGTGACGTAGAAAGTAATAATTTCTTGG

GTAGTTTGCAGTTTTAAAATTATGTTTTAAAATGGACTATCATATGCTTACCGTAACTTGAAAGTATTTC

GATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAGGTACCGGTCCGCAGGTATGCACGCGTGAATTCT

AGATCTTGAGACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGC

AGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAA

ATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAGATCCACTTTGGCGCCGGCTCGAGGGGG

Table S7. shRNA lentiviral vectors used for individual validation assay
shRNA ID shRNA sequence Fluoresce Resistanc

nt protein e

PIK3CA_sh1 CCGGGCACAATCCATGAACAGCATTCTCGAGAATGCTGTTCATGGATTGTGCTTTT mkate NeoR

PIK3CA_sh2 CCGGGCATTAGAATTTACAGCAAGACTCGAGTCTTGCTGTAAATTCTAATGCTTTTT mkate NeoR

PIK3CA_sh3 CCGGGAATTGGAGATCGTCACAATACTCGAGTATTGTGACGATCTCCAATTCTTTTT mkate NeoR

NFKB1_sh1 CCGGCGCCTGAATCATTCTCGATTTCTCGAGAAATCGAGAATGATTCAGGCGTTTT EYFP puroR

NFKB1_sh2 CCGGGCCTGAACAAATGTTTCATTTCTCGAGAAATGAAACATTTGTTCAGGCTTTTT EYFP puroR

30
NFKB1_sh3 CCGGCCTTTCCTCTACTATCCTGAACTCGAGTTCAGGATAGTAGAGGAAAGGTTTT EYFP puroR

CDK4_sh1 CCGGCCTTCCCATTTCTCTACACTACTCGAGTAGTGTAGAGAAATGGGAAGGTTTT EYFP puroR

CDK4_sh2 CCGGCCTAGATTTCCTTCATGCCAACTCGAGTTGGCATGAAGGAAATCTAGGTTTT EYFP puroR

CDK4_sh3 CCGGAGGACATATCTGGACAAGGCACTCGAGTGCCTTGTCCAGATATGTCCTTTTT EYFP puroR

MYC_sh1 CCGGCCATAATGTAAACTGCCTCAACTCGAGTTGAGGCAGTTTACATTATGGTTTTT mkate NeoR

MYC_sh2 CCGGCAGTTGAAACACAAACTTGAACTCGAGTTCAAGTTTGTGTTTCAACTGTTTT mkate NeoR

MYC_sh3 CCGGCCTGAGACAGATCAGCAACAACTCGAGTTGTTGCTGATCTGTCTCAGGTTTT mkate NeoR

IL6R_sh1 CCGGGCAGGCACTTACTACTAATAACTCGAGTTATTAGTAGTAAGTGCCTGCTTTTT EYFP puroR

IL6R_sh2 CCGGCTCTGGAAACTATTCATGCTACTCGAGTAGCATGAATAGTTTCCAGAGTTTTT EYFP puroR

IL6R_sh3 CCGGAGCCCTTATGACATCAGCAATCTCGAGATTGCTGATGTCATAAGGGCTTTTTT EYFP puroR

TNF_sh1 CCGGCTGTAGCCCATGTTGTAGCAACTCGAGTTGCTACAACATGGGCTACAGTTTT mkate NeoR

TNF_sh2 CCGGCAGGTCTACTTTGGGATCATTCTCGAGAATGATCCCAAAGTAGACCTGTTTT mkate NeoR

TNF_sh3 CCGGCCTCTCTCTAATCAGCCCTCTCTCGAGAGAGGGCTGATTAGAGAGAGGTTT mkate NeoR

TT

Control CCGGCAACAAGATGAAGAGCACCAACTCGAGTTGGTGCTCTTCATCTTGTTGTTTT EBYP puroR

Table S8. Candidate genes linking inflammation to cancer

Cipher Cipher
Gene DEG
IBD CRC Literature KEGG Pathway
Symbol adj.P.Val
Rank Rank
0.00140148 hsa05321, hsa04620, hsa04630,
STAT1 75
9 hsa05200
MSH2 81 hsa05210, hsa05200
MOK Literature
E2F1 30 hsa05200
MAP3K1
67 hsa04010
1
0.00089353
HIF1A Literature hsa04066, hsa05200, hsa04150
3
0.02415950
REL Literature hsa04014
1

31
 0.04473917
PTGS2 Literature hsa04064, hsa05200, hsa04668
2
hsa04014, hsa04620, hsa05210,
MAPK9 36 0.04184329
hsa05200, hsa04010, hsa04668
BRCA1 61 10 hsa04151
IL1R1 59 53 hsa04064, hsa04010
0.00459943 hsa05321, hsa04630, hsa04066,
STAT3 32 Literature
6 hsa05200
TSLP 28 hsa04630
hsa04014, hsa04620, hsa04630,
PIK3R3 80 1.51E-05 hsa04066, hsa05210, hsa05200,
hsa04668, hsa04150, hsa04151
IFNL3 11 hsa04630
IFNL1 12 hsa04630
0.02816749
BTK 93 hsa04064
7
APC 42 hsa05210, hsa05200
0.04094500 hsa04064, hsa05200, hsa04010,
TRAF2 Literature
5 hsa04668
hsa05210, hsa05200, hsa04010,
BRAF Literature
hsa04150
0.00938998
IFNAR2 65 hsa04620, hsa04630, hsa04151
6
0.01042399
S1PR1 Literature
7
IL10 13 hsa05321, hsa04630
0.00042040
IL18R1 38 24 hsa05321, hsa04668
7
0.01637780
SRC Literature
9
hsa04014, hsa04620, hsa04064,
IKBKB 82 Literature hsa05200, hsa04010, hsa04668,
hsa04150, hsa04151
HMGB1 Literature
TNFRSF 0.02339707
Literature hsa04064, hsa04010, hsa04668
1A 1
0.04638891
CDK4 66 hsa05200, hsa04151
6
ATM 60 hsa04064

32
 0.01207761
IL12RB1 36 hsa05321, hsa04630
7
IL22RA2 18 hsa04630
JUNB 73 13 hsa04668
NOD2 2 hsa05321, hsa04668
AR 49 hsa05200
hsa04014, hsa04620, hsa04630,
PIK3CA 15 hsa04066, hsa05210, hsa05200,
hsa04668, hsa04150, hsa04151
IL23R 4 hsa05321, hsa04630
IL10RB 7 hsa04630
IL21 48 hsa05321, hsa04630
0.02583726
IL21R 44 hsa05321, hsa04630
7
RBL1 56 hsa04350
RELB Literature hsa04064, hsa04010
hsa05321, hsa04014, hsa04620,
NFKB1 Literature hsa04064, hsa04066, hsa05200,
hsa04010, hsa04668, hsa04151
hsa04014, hsa05200, hsa04010,
HRAS 86
hsa04151
0.04053150
JAK1 37 hsa04630, hsa05200, hsa04151
2
0.01609893
IL6R 94 Literature hsa04630, hsa04066, hsa04151
1
0.02610025
DCC 100 hsa05210, hsa05200
2
0.01000918
IL23A 5 hsa05321, hsa04630
9
0.02785496
JAK2 35 hsa04630, hsa04151
6
IL3 60 hsa04630, hsa04151
0.02887017
SPHK1 Literature
1
0.00112182
STAT5A 56 hsa04630, hsa05200
3
0.01654981
PML 74 hsa05200
7

33
 0.00395870
MCL1 12 hsa04151
1
IFNL2 9 hsa04630
TBK1 Literature hsa04014, hsa04620
IRF3 Literature hsa04620
FADD 71 hsa04620, hsa05200, hsa04668
RET Literature hsa05200
STMN1 40 hsa04010
RALB Literature hsa04014, hsa05200
hsa05321, hsa05210, hsa05200,
SMAD3 28
hsa04350
hsa04014, hsa05210, hsa05200,
KRAS Literature
hsa04010, hsa04151
hsa05321, hsa04620, hsa04630,
0.01957845
IL6 Literature hsa04066, hsa05200, hsa04668,
8
hsa04151
ATF2 39 hsa04010, hsa04668, hsa04151
0.00142399
IL10RA 1 hsa04630
4
0.03425432
E2F4 59 hsa04350
7
SP1 27 hsa04350
0.01577333
NFKB2 Literature hsa04064, hsa05200, hsa04010
2
hsa04014, hsa04620, hsa04630,
0.04912775
PIK3R1 95 87 hsa04066, hsa05210, hsa05200,
7
hsa04668, hsa04150, hsa04151
MBTPS1 Literature
0.03144691 hsa04630, hsa05210, hsa05200,
CCND1 6
4 hsa04151
FGFR4 53 hsa04014, hsa04010, hsa04151
CTBP1 92 0.02271873 hsa05200
hsa05210, hsa05200, hsa04010,
TP53 Literature
hsa04151
IL22RA1 17 hsa04630
0.04462672
AXIN2 1 hsa05210, hsa05200
7

34
 hsa05321, hsa04014, hsa04620,
RELA Literature hsa04064, hsa04066, hsa05200,
hsa04010, hsa04668, hsa04151
0.01097072
LCK 68 hsa04064
9
0.03962791 hsa04630, hsa05210, hsa05200,
MYC 9 Literature
8 hsa04010, hsa04350, hsa04151
0.04721854
MSH6 79 3 hsa05210, hsa05200
2
VHL Literature hsa04066, hsa05200
hsa05321, hsa04620, hsa04064,
TNF Literature 0.02873972 hsa04010, hsa04350, hsa04668,
hsa04150
IL22 16 Literature hsa05321, hsa04630

Table S9. Functional enrichment analysis of candidate PPI network

Category Term Count % P-Value Benjamini
GOTERM_B
intracellular signal transduction 61 72.6 2.30E-30 3.80E-27
P_4
GOTERM_B
response to cytokine 39 46.4 2.70E-28 2.30E-25
P_4
GOTERM_B
signal transduction 77 91.7 6.40E-28 3.60E-25
P_4
GOTERM_B positive regulation of signal
46 54.8 1.10E-26 4.60E-24
P_4 transduction
GOTERM_B positive regulation of
59 70.2 2.00E-26 6.70E-24
P_4 macromolecule metabolic process
GOTERM_B positive regulation of cellular
58 69 1.60E-25 4.60E-23
P_4 metabolic process
GOTERM_B positive regulation of cell
46 54.8 3.90E-25 9.40E-23
P_4 communication
GOTERM_B positive regulation of cytokine
28 33.3 4.30E-24 9.20E-22
P_4 production
GOTERM_B
regulation of signal transduction 55 65.5 2.40E-23 4.50E-21
P_4
GOTERM_B
programmed cell death 47 56 5.40E-23 9.00E-21
P_4
GOTERM_B cellular response to organic
50 59.5 6.90E-23 1.10E-20
P_4 substance
35
GOTERM_B positive regulation of intracellular
36 42.9 9.30E-23 1.30E-20
P_4 signal transduction
GOTERM_B regulation of programmed cell
42 50 1.50E-22 1.90E-20
P_4 death
GOTERM_B regulation of intracellular signal
45 53.6 2.30E-22 2.80E-20
P_4 transduction
GOTERM_B
response to other organism 34 40.5 6.90E-22 7.70E-20
P_4
positive regulation of
GOTERM_B
macromolecule biosynthetic 43 51.2 1.50E-21 1.50E-19
P_4
process
GOTERM_B positive regulation of cellular
44 52.4 3.20E-21 3.20E-19
P_4 biosynthetic process
GOTERM_B
regulation of defense response 31 36.9 4.00E-21 3.80E-19
P_4
GOTERM_B positive regulation of biosynthetic
44 52.4 6.40E-21 5.70E-19
P_4 process
GOTERM_B positive regulation of nitrogen
44 52.4 7.50E-21 6.30E-19
P_4 compound metabolic process
GOTERM_B cell surface receptor signaling
51 60.7 5.40E-20 4.40E-18
P_4 pathway
GOTERM_B positive regulation of gene
42 50 1.20E-19 9.30E-18
P_4 expression
GOTERM_B positive regulation of protein
40 47.6 1.60E-19 1.20E-17
P_4 metabolic process
GOTERM_B regulation of phosphorus metabolic
41 48.8 1.80E-19 1.30E-17
P_4 process
positive regulation of nucleobase-
GOTERM_B
containing compound metabolic 41 48.8 5.10E-19 3.40E-17
P_4
process
GOTERM_B positive regulation of cellular protein
38 45.2 1.60E-18 1.10E-16
P_4 metabolic process
GOTERM_B positive regulation of phosphorus
33 39.3 9.20E-18 5.70E-16
P_4 metabolic process
GOTERM_B positive regulation of RNA
37 44 1.30E-17 7.70E-16
P_4 metabolic process
GOTERM_B
inflammatory response 27 32.1 2.50E-17 1.40E-15
P_4

36
Table S10. Differential genetic interaction network
Symbol1 Symbol2 Sign Pheno1 Pheno2 Pheno12 avgGI
APC CDK4 N 0.184801135 0.139979735 -0.519847455 -0.851012551
APC IL22RA1 N 0.184801135 0.364968911 -0.501790995 -1.049677905
APC IL22 N 0.184801135 0.117830181 -0.867990406 -1.14057327
APC PIK3CA N 0.184801135 -0.111547492 -0.829667613 -0.869397995
AR BRCA1 N 0.239201946 0.2697007 -0.47251278 -0.986696237
TNFRSF
AR N 0.239201946 -0.115259463 -0.801745085 -0.863076029
1A
ATF2 JAK1 N -0.115166013 -0.201428117 -1.572132434 -1.31734377
ATM IL6R N -0.110224554 0.08498628 -0.878132816 -0.837373825
ATM NOD2 N -0.110224554 -0.129642089 -1.061519795 -0.87838825
BRCA1 IKBKB N 0.2697007 0.038416414 -0.559267093 -0.831224041
BRCA1 IL22RA2 N 0.2697007 -0.096791846 -1.020116096 -1.114841263
BRCA1 VHL N 0.2697007 0.080725297 -0.715973783 -1.066285826
BTK FADD N -0.217962488 -0.416094306 -1.507799493 -1.019599628
CDK4 MYC N 0.139979735 0.004385368 -1.135878349 -1.252638963
CDK4 TP53 N 0.139979735 -0.305504887 -1.181756356 -0.938589737
E2F1 IL1R1 N 0.130552143 -0.24109431 -1.441007671 -1.296290374
E2F1 JAK1 N 0.130552143 -0.201428117 -1.309035081 -1.20741079
E2F1 MBTPS1 N 0.130552143 0.016050186 -0.70346245 -0.836652264
E2F4 NOD2 N -0.326225172 -0.129642089 -1.373925002 -1.032739038
FADD IRF3 N -0.416094306 0.006996782 -1.421370219 -1.056943592
FGFR4 IL22RA1 N -0.086507835 0.364968911 -0.62867383 -0.841624845
FGFR4 PIK3R1 N -0.086507835 -0.188824592 -1.230536924 -0.991401233
FGFR4 SRC N -0.086507835 -0.37076877 -1.779803637 -1.408921823
HRAS IL22RA1 N -0.032794091 0.364968911 -0.574719205 -0.833516128
MAP3K1
IFNAR2 N -0.158068835 -0.179160579 -1.266532638 -1.010886559
1
IFNL1 LCK N 0.085419431 -0.075341626 -1.086015009 -1.089389418
IFNL1 VHL N 0.085419431 0.080725297 -0.677731687 -0.835392139
IL10RA S1PR1 N -0.068570186 0.177287631 -1.162156477 -1.238544282
IL10 MCL1 N -0.206636335 0.117890985 -1.471078194 -1.362128609
IL12RB1 IL6 N -0.350260257 -0.085536212 -1.477619531 -1.121225158
IL21R LCK N 0.117898133 -0.075341626 -1.025138104 -1.060621275
IL22RA1 VHL N 0.364968911 0.080725297 -0.517131361 -0.970193212
IL22RA2 STAT3 N -0.096791846 -0.024024598 -1.003327393 -0.902167327

37
IL22 NOD2 N 0.117830181 -0.129642089 -1.015521945 -0.996486766
IL6R LCK N 0.08498628 -0.075341626 -0.904265004 -0.905331907
IL6R PIK3R3 N 0.08498628 0.037127637 -0.931364334 -1.04107283
IL6R TNF N 0.08498628 -0.12554521 -1.349064352 -1.298032663
IRF3 S1PR1 N 0.006996782 0.177287631 -0.747504696 -0.911965017
TNFRSF
MCL1 N 0.117890985 -0.115259463 -0.913268672 -0.890406961
1A
MOK STAT1 N -0.025093033 0.058739673 -0.830580988 -0.860297952
MSH2 VHL N -0.085174793 0.080725297 -0.938099479 -0.92173246
MYC STAT3 N 0.004385368 -0.024024598 -1.36950383 -1.354083142
NFKB2 PML N -0.207800156 -0.210120415 -1.209916139 -0.902459828
RELB S1PR1 N 0.030455118 0.177287631 -0.709948383 -0.884040858
TNFRSF
VHL N -0.115259463 0.080725297 -1.148417886 -1.09356405
1A
APC DCC P 0.184801135 -0.223066142 1.142940065 1.200268254
AR IL23R P 0.239201946 -0.061717246 1.80080488 1.654167548
BRAF SRC P -0.214325228 -0.37076877 0.748430603 1.148035676
BRCA1 RELA P 0.2697007 -0.20656992 1.338460504 1.319581079
DCC IFNL3 P -0.223066142 -0.15690531 1.311036803 1.577911694
DCC IL10RA P -0.223066142 -0.068570186 0.914005881 1.153793773
E2F1 PML P 0.130552143 -0.210120415 1.071095317 1.182757928
E2F4 FADD P -0.326225172 -0.416094306 1.450205746 1.924000307
E2F4 IL10RB P -0.326225172 -0.104768861 1.754847113 2.047881907
E2F4 PIK3CA P -0.326225172 -0.111547492 1.005330098 1.32539235
E2F4 TP53 P -0.326225172 -0.305504887 1.373830585 1.763619424
IFNL1 MOK P 0.085419431 -0.025093033 1.263660863 1.210493427
IFNL3 IL12RB1 P -0.15690531 -0.350260257 0.996260849 1.315912881
IFNL3 MYC P -0.15690531 0.004385368 1.068341883 1.191139113
IFNL3 NOD2 P -0.15690531 -0.129642089 1.370573915 1.578359132
TNFRSF
IFNL3 P -0.15690531 -0.115259463 1.344330627 1.531953176
1A
IL10RA NFKB1 P -0.068570186 -0.157535549 1.393944623 1.575342433
IL10RB PIK3CA P -0.104768861 -0.111547492 1.050519136 1.210694052
IL10RB SRC P -0.104768861 -0.37076877 1.219200316 1.548354384
TNFRSF
IL10RB P -0.104768861 -0.115259463 1.322694284 1.481335795
1A
IL10 NFKB2 P -0.206636335 -0.207800156 1.049559501 1.363721638
IL10 SPHK1 P -0.206636335 -0.294009785 0.938207887 1.308417306

38
IL12RB1 PML P -0.350260257 -0.210120415 0.887678515 1.268000347
IL12RB1 SPHK1 P -0.350260257 -0.294009785 0.866344129 1.311763568
TNFRSF
IL18R1 P -0.108242199 -0.115259463 1.029441937 1.200420529
1A
IL21R PIK3R1 P 0.117898133 -0.188824592 1.252993931 1.304086959
IL22RA2 SP1 P -0.096791846 -0.233407894 0.954556893 1.197785559
IL6 JAK1 P -0.085536212 -0.201428117 1.87615062 2.110388431
IRF3 RALB P 0.006996782 -0.115281595 1.456887788 1.553698874
JAK1 NFKB1 P -0.201428117 -0.157535549 1.161491482 1.424807475
JAK1 PML P -0.201428117 -0.210120415 1.309584707 1.600232343
JAK1 SMAD3 P -0.201428117 0.445464668 1.41938675 1.272237459
JAK1 TNF P -0.201428117 -0.12554521 1.565804293 1.810717148
MCL1 S1PR1 P 0.117890985 0.177287631 1.419196759 1.1302387
MSH2 RELA P -0.085174793 -0.20656992 0.957371025 1.204552486
NFKB1 PIK3CA P -0.157535549 -0.111547492 1.449572534 1.655615832
NFKB1 PTGS2 P -0.157535549 -0.196496883 1.05369656 1.315835175
NOD2 RBL1 P -0.129642089 -0.165569291 1.965500021 2.209217498
PTGS2 SRC P -0.196496883 -0.37076877 0.905992007 1.302201936

Table S11. Ranking effects of four compounds from traditional Chinese

medicine Liu-Wei-Di-Huang analogous prescriptions on inflammation-
induced tumorigenesis by experimental and prediction methods,
respectively.
Example Compound sources Analogous Experimen Prediction
compounds prescriptions tal rank rank
Quercetin Cortex Moutan 6 Liu-wei-di- 1 1st interval
Cornus officinalis 7 huang
Kaempferol Cornus officinalis 7 Liu-wei-di- 2 3rd interval
huang
Isorhamnetin Cortex Moutan 8 Liu-wei-di- 3 2nd interval
huang,
Astragali Radix 9 Ba-wei-di-
huang
Albiflorin Radix paeoniae Alba 10 Gui-shao-di- 4 4th interval
huang

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