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Supplemental Material
Supplemental Figures
Figure S1. Alteration frequencies of individual INO80 subunits in lung adenocarcinoma
and squamous carcinoma. Data was obtained from The Cancer Genome Atlas portal:
http://www.cbioportal.org.
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Figure S2. Ino80 silencing in NSCLCs. (A) A549 cells were infected with non-targeting
(shNT) or Ino80 (shIno80) shRNAs, and Ino80 expression was determined by western blot.
(B-C) Inhibition of NSCLC cell growth by additional Ino80 shRNAs. A549, H23, H358,
H1299, H1703 cells were transduced with indicated shRNA viruses and cell growth was
determined at the indicated time points. Data was plotted as Mean ± SEM from 3
independent experiments. (D) Silencing of Ino80 in normal human bronchial epithelial cells
NHBE and cell lines BEAS-2B. Cells were transduced non-targeting (NT) or Ino80 shRNA
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(shIno80) viruses and cell growth was determined at the indicated time points. Data was
plotted as Mean ± SEM from 3 independent experiments.
Figure S3. Statistical analysis of clonogenesis assay and anchorage-independent growth
for NSCLC cells. (A) Statistical analysis of clonogenesis assay for H385, H1299, H1703,
and H23 cells transduced with shNT, shIno80, shIno80-2 viruses. (B) Statistical analysis of
anchorage-independent growth for H385, H1299, H1703, and H23 cells transduced with
shNT, shIno80, shIno80-2 viruses. For H358 cells, both the number and size of colonies were
analyzed. H23 cells were not included in the analysis as they did not form colonies in softagar culture.
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Figure S4. H2A.Z and H3K56ac genomic occupancy. A549 cells were transduced with
shNT (NT) or shIno80 (Ino80KD) viruses, and H2A.Z (upper panel) or H3K56ac (lower
panel) genomic occupancy near transcription start site (TSS) was determined by ChIP-seq.
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Table S1. Primers used in our study
RT-qPCR
hIno80 qpcr Left
TAACCGGGACCCCAATTC
hIno80 qpcr Right
GGCATAATGAAATGCAGCAG
hCXCL5_Left
GGTCCTTCGAGCTCCTTGT
hCXCL5_Right
ACGCAGCTCTCTCAACACAG
hMAP3K1_Left
CACCACCACTGCATGTCAA
hMAP3K1_Right
GATCTACAAAGGGGACATATTAAAGG
hSEC62_Left
AGTATTCTTCTCCTTGCTGTTGC
hSEC62_Right
GGCAAGAACCAAAAGTGGTG
hZNF703_Left
CAAGGACACCCGAAAGCA
hZNF703_Right
CGCTCAGCATCTTCAGGAC
hCTNNB1_Left
ACAGAGACTCAGACCCTGGC
hCTNNB1_Left
GCCGGTGCACACTCACTTTT
hCXCL5_P1_Left
AGCAAAAATAGAAATTCACAACCA
hCXCL5_P1_Right
TGACACTTGTGAAAAGGCTTGTA
hCXCL5_P2_Left
CACTCATGAGATACCAAGGTTGAA
hCXCL5_P2_Right
TGTGACCTTGGCAAGAGAGA
hMAP3K1_P1_Left
GCTTATATCTTAACCCAGGCAGTC
hMAP3K1_P1_Right GTATGGCACAGCGATCAGG
hMAP3K1_P2_Left
TCGGTAACGCCTGTCAAAG
hMAP3K1_P2_Right AACCGCACTTCCTAAAAGACTG
hSEC62_P1_Left
ChIP-qPCR hSEC62_P1_Right
hSEC62_P2_Left
GCAGGAGGGTTGCTTGAG
GGGGTCTCATTGTGTTGCAT
AACAACCACAACCTCGTTGG
hSEC62_P2_Right
CACACTGGCATGTGAAAGGT
hZNF703_P1_Left
AGGGTGGAGGGTGTGTGTAA
hZNF703_P1_Right
CCTTCTTAGCCCCCTTAGCA
hZNF703_P2_Left
CGCGGTACAGTGAGGAACTT
hZNF703_P2_Right
TCGGTGTCTGGTGTGTTACAG
hCTNNB1_P1_Left
GCACAAGTGAGCACTGAGAAAG
hCTNNB1_P1_Right GCACACTCTGCAGACTTTCATG
hCTNNB1_P2_Left
ACCCCTGTCGGATTTTACTTCC
hCTNNB1_P2_Right TAAGAAGCTACTGCGGCTGTC
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Table S2. IPA of DEGs after Ino80 KD by shRNA at day 4
Diseases or Functions Annotation
-Log10 (p value)
malignant solid tumor
17.92812
cancer
17.6216
abdominal neoplasm
11.82102
abdominal cancer
11.77989
neoplasia of epithelial tissue
11.72125
epithelial cancer
10.97881
tumorigenesis of tissue
10.67778
digestive organ tumor
9.374688
digestive system cancer
9.166853
Gastrointestinal Tract Cancer and Tumors 8.552842
pelvic cancer
8.216096
breast or ovarian cancer
8.155523
adenocarcinoma
8.100179
gastrointestinal tract cancer
7.866461
breast or colorectal cancer
7.628932
development of genitourinary system
7.568636
development of urinary tract
7.533132
urogenital cancer
7.390406
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Table S3. IPA of predicted upstream regulators after Ino80 KD at day 4
Upstream Regulator
HIF1A
tretinoin
troglitazone
dexamethasone
HNF1B
ERBB2
MGEA5
HNRNPA2B1
AHR
beta-estradiol
calcitriol
TP53
decitabine
trans-hydroxytamoxifen
EPAS1
TNF
CTNNB1
TGFB1
-Log10 (p value)
9.600326
9.476254
7.705534
7.432974
7.221126
7.071604
6.974694
6.943095
6.764472
6.462181
6.425969
6.380907
6.048177
5.896196
5.872895
5.815309
5.725842
5.621602
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Table S4. IPA of Ino80-occupied genes
Diseases or Functions Annotation
expression of RNA
transcription
transcription of RNA
malignant solid tumor
cancer
transcription of DNA
cell death of tumor cell lines
abdominal neoplasm
proliferation of cells
abdominal cancer
processing of RNA
epithelial cancer
tumorigenesis of tissue
activation of DNA endogenous promoter
cell death
neoplasia of epithelial tissue
apoptosis
cell cycle progression
-Log10 (p value)
50.17263
45.50307
42.451
33.93554
33.8041
32.81248
29.86328
29.17393
28.767
27.97469
27.92082
27.39041
26.58336
26.43533
26.35655
26.2993
26.23136
26.04915
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Table S5. IPA of potential Ino80 target genes
Diseases or Functions Annotation
cancer
malignant solid tumor
abdominal cancer
tumorigenesis of tissue
digestive system cancer
epithelial cancer
abdominal neoplasm
digestive organ tumor
neoplasia of epithelial tissue
development of body trunk
abnormal morphology of thoracic cavity
invasion of cells
gastrointestinal tract cancer
Gastrointestinal Tract Cancer and Tumors
synthesis of lipid
expression of RNA
proliferation of cells
formation of kidney
-Log10 (p value)
11.0716
10.70774
6.636388
6.628932
6.600326
6.420216
6.291579
6.281498
6.216811
6.022734
5.642065
5.596879
5.521434
5.492144
5.462181
5.235824
5.226214
5.043832
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Table S6. Datasets used for analysis
Factor
H3K4me3
H3K4me1
H3K27ac
p300
H3K27me3
DNase I
Signal Track Used
A549 EtOH H3K4me3
A549 EtOH H3K4me1
A549 EtOH H3K27ac
A549 p300 EtOH
A549 p300 EtOH
A549 EtOH H3K27me3
GEO Accession
GSM1003561
GSM1003453
GSM1003578
GSM1010827
GSM1003455
GSM816649
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