Cell Reports, Volume 15

Supplemental Information

SET9-Mediated Regulation of TGF-b Signaling

Links Protein Methylation to Pulmonary Fibrosis
Maximilianos Elkouris, Haroula Kontaki, Athanasios Stavropoulos, Anastasia
Antonoglou, Kostas C. Nikolaou, Martina Samiotaki, Eszter Szantai, Dimitra
Saviolaki, Peter J. Brown, Paschalis Sideras, George Panayotou, and Iannis Talianidis
A B
Probe
RV WT ES
NcoI RV
3 4 5 NcoI 5’ 3’
WT
allele NcoI 15.7 11.5 kb
5’ probe 3’ probe
RV NcoI RV 11.5
Targeting 7.2 kb
vector NEO

C
NcoI RV RV NcoI RV
NcoI
Targeted
allele NEO
Probe +/+ -/-
5’ probe 3’ probe
5’ 3’ Wt , 1951bp
+ CMV-CRE
NcoI 8.9
NcoI RV RV
NcoI
Null RV 7.2
Null , 223bp
allele

D E

F
Lung fibroblast mRNA
WT Set9-KO WT+(R)-PFI-2

HmgA2 Has2 Twist Snai1

9
8
Rel. mRNA levels

4 4 4
7
3 3 * * 3 * 6
*
* * ** 5 **
2 * * 2 * * 2 * 4 *
* * * * 3 * * **
* * * * * *
1 ** * 1 * 1 ** 2
** 1 **
TGF-β 0 1 2 6 12 (h) 0 1 2 6 12 (h) 0 1 2 6 12 (h) 0 1 2 6 12 (h)

G H
H1299 mRNA
WT sh-Set9

COL7A1 SERPNE1 CTGF

14 8
8
Rel. mRNA levels

12
10 6
6
8
4 4
6
4 * 2 *
* * * 2 *
2 * * *
* *
TGF-β 0 2 6 12 (h) 0 2 6 12 (h) 0 2 6 12 (h)
Figure S1 (Related to Figure 1)

(A) Strategy of targeting the Setd7 alleles in mouse ES cells. The region spanning exon 3-5 of the
Setd7 wild type and targeted allele is shown. Exons are presented as green boxes. LoxP sites
flanking exon 4 and the neomycin (NEO) selection cassette are shown as red triangles. The
positions of the 3’ and 5’ probes, the restriction enzyme sites used for genotyping and the expected
fragment sizes are indicated.

(B) Representative southern blot analysis confirming homologous recombination in the positive ES
clone used for the production of chimeric mice.

(C) PCR-based genotyping using primers of wild type (+/+) and null (-/-) alleles of the targeted
locus. The locations of the primers are indicated with blue arrows in S1A.

(D) Set9 expression levels are not affected by TGF-β treatment.

Primary lung fibroblasts from wild type (WT) and Set9-KO mice were left untreated or treated with
5 ng/ml TGF-β for the indicated time periods. Whole cell extracts were analyzed in western blots
using antibodies against Set9 (upper panel) and TFIIB (lower panel).

(E) Wild type (WT) and Set9-depleted (shSet9) Hela cells were left untreated or treated with 5
ng/ml TGF-β and/or with 1 µM (R)-PFI-2 inhibitor, as indicated. Whole cell extracts were analyzed
in western blots using antibodies against Set9 (upper panel) and TFIIB (lower panel).

(F) qPCR analysis of the mRNA levels of the indicated panel of genes involved in Epithelial-
Mesenchymal Transition (HmgA2, Has2, Twist, Snai1) in isolated primary lung fibroblasts that
were treated in vitro with 5 ng/ml TGF-β for the indicated time periods (h= hours). Lung fibroblasts
were from wild type (WT) mice (black bars) or Set9-KO mice (grey bars). Wild type mice treated
with 1 µM (R)-PFI-2 Set9 inhibitor (white bars). Bars represent mean values of mRNA levels
normalized to Gapdh mRNA ± sem, from 4 experiments performed in triplicates. * p value < 0.05.
(two-tailed Student’s t-test).

(G) Primary lung fibroblasts were left untreated (-) or treated with 5 ng/ml TGF-β (+) for 6 hours.
Whole cell extracts were subjected to western blot analysis using antibodies against p53 or
GAPDH.

(H) Wild type and sh-Set9-expressing H1299 human lung carcinoma cells were treated with 5
ng/ml TGF-β for the indicated time points. The mRNA levels of COL7A1, SERPINE1 and CTGF
were evaluated by qPCR. Bars represent mean values of mRNA levels normalized to GAPDH
mRNA ± sem from 4 experiments performed in triplicates. * p value < 0.05. (two-tailed Student’s t-
test).
A

.2

.1

.0

.9

.9

.8

.8

.7

.7

.6

.5

.5
.0

.6

2
4

1
85

14

72

77

40

03

06

69

72

75

87

30
15

74

9.

2.

0.

3.

6.

5.

6.

5.

0.
1.

7.
23

23

21

21

19

18

17

16

14

13

12

10

10

95

90

76

70

64

57

44

37

26
11

83

14
25 24 23 22 21 20 19 18 17 16 15 14 13 12 11 10 9 8 7 6 5 4 3 2 1 y'

G A K G H H H P H P P T S G A G A A G G A E A D L K
b' 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25

.5

.6

.7

.7

.7

.8

.7

.8

.8

.9

.9

.9

.0

.0

.1
.6
1

5
.0

9.

1.

8.

5.

2.

9.

6.

3.

70

68

55

12

83

40

55

82

39

96

67

96

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83

96
67
58

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60

73

83

97

10

12

13

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15

13

16

17

17

18

19

20

21

22
11
350
ITMS 50
FTMS
815.0734@cid35.00 m/z=814.73883 Da, z=+3 815.07343
MH+=2442.20194 Da z=3

300 40

Intensity (counts x10-3)

Isolation window

30
815.40741
250 z=3
814.73883
z=3
b242+ -H2O
20 Monoisotopic mass
Intensity (counts)

1083.99 b242+ 815.74347

200 b172+ -H2O z=3
b 7+ 1092.84
b112+ 797.38 10
739.36
584.20 b 9+ 816.07733
b193+ y243+ z=3
150 973.59 0
581.30 772.23 810 812 814 816 818 820
y253+
m/z
b92+ y243+ -NH 795.52
100
487.34 767.06
y242+
b222+
1157.98 [M+2H]2+ -H2O
b5 + b233+ 998.61
1211.85
50 465.46 689.64

0
200 600 1000 1400 1800
m/z

B C
Figure S2 (Related to Figure 2)
(A) Identification of the K70 methylation site by mass-spectrometry. Recombinant Smad7 protein
was methylated in vitro and digested with trypsin. Tryptic peptides were subjected to LC-MS/MS
analysis.
Top: Sequence of the tryptic peptide GAKmeGHHHPHPPTSGAGAAGGAEADLK, indicating the
theoretical masses of singly-charged b’ and y’ fragment ions. The main figure shows fragmentation
mass spectrum analysis of the peptide by ion-trap MS, with arrows pointing at b’ (red) or y’ (blue)
fragments that contain the methylated K70. A dehydrated parent ion is shown in green. The insert
shows the accurate mass spectrum of the peptide, obtained by Fourier transform MS in the Orbitrap,
with the isolation window indicated in yellow. The ion had a positive charge of 3. The
corresponding monoisotopic mass was 14.01546 Da heavier than the theoretical mass of the
peptide, indicating the presence of a methyl group.

(B) qPCR analysis of the mRNA levels of the indicated panel of ECM genes in wild type HeLa
cells (WT) and HeLa cells stably expressing sh-Set9 (sh-Set9). The cells were transfected with
control siRNA (Ctr. siRNA) or Smad7 siRNA pool. Three days after transfection, the cells were
treated with TGF- for 0 or 6 hours, as indicated. Bars represent mean values of mRNA levels
normalized to GAPDH mRNA ± sem from 4 experiments performed in triplicates.
* p value < 0.05. ** p value < 0.005 (two-tailed Student’s t-test).

(C) Wild type (WT) and sh-Set9 expressing (sh-Set9) HeLa cells were transfected with Smad7-
specific smart pool siRNAs or control siRNA, as indicated. Three days after transfection
endogenous levels of Smad7 and GAPDH proteins were evaluated by western blot analysis.
 GST-Set9 + - + + - +
His-Smad7 WT + + - + + -
His-Smad7 K70R - - + - - +
kD 200
116
97
66
45

31

Western Blot: αMe-Smad7 αSmad7

Figure S3 (Related to Figure 3)

Specificity of αMe-Smad7 antibody. 10 ng of recombinant 6xHis-tagged wild type and K70R mutant
forms of Smad7 proteins were methylated in vitro with 100 ng GST-Set9 and 1 µM cold SAM. The
reaction products were analyzed in western blots using αMe-Smad7 or αSmad7 antibodies. Note that the
αMe-Smad7 did not recognize non-methylated Smad7 proteins (lanes 2-3 in left panel).

Lung
HeLa fibroblasts

kD 200
116
97
66
TGF-β-RI
45

31

WB: αTGF-β-RI

WB: αGAPDH

Figure S4 (Related to Figure 4)

Set9 depletion reduces TGF-β-RI protein levels. Wild type (WT) and sh-Set9 Hela cells or wild type (WT)
and Set9-KO lung fibroblasts were treated with 5 ng/ml TGF-β for 6 hours. The endogenous levels of
TGF-β-RI protein were evaluated in western blots using antibodies against TGF-β-RI (upper panel) and
GAPDH (lower panel).
 A Control (PBS) Bleomycin

WT
Set9-KO

100 µm Masson’s trichrome

B
WT SET9-KO
20
Control (PBS) Bleomycin Control (PBS) Bleomycin
16

CD45+ cells
12
8
4

C Ble
100 µm 100 µm
24
20
αSma+ cells

16
12
8
4

αSma / CD45 / DAPI 25 µm αSma / CD45 / DAPI 25 µm C Ble

Figure S5 (Related to Figure 5)

(A) Masson’s trichrome reagent staining of 12 week-old wild type (WT) and Set9-KO (Set9-KO) mice
that were treated intratracheally with PBS or 0.33 units bleomycin for 15 days, as indicated. Note the
much smaller fibrotic areas (collagen – blue and keratin – red) in the lungs of bleomycin-treated Set9-KO
mice compared to similarly treated wild type mice.
(B) Bleomycin-dependent inflammation and activation of lung myofibroblasts are not affected by Set9
inactivation. 12 week-old wild type (WT) and Set9-KO (Set9-KO) mice were treated intratracheally with
PBS or 0.33 units bleomycin for 15 days, as indicated. Representative staining of lung sections with the
myofibroblast marker (αSma) and the pan-leukocyte marker (CD45) are shown.
Panels at right: Quantitation of CD45+ and αSma+ cells in 20 high power fields of control, PBS-treated
(C) or bleomycin-treated (Ble) samples. Note that Set9 inactivation does not affect significantly
bleomycin-induced accumulation of αSma+ or CD45+ cells in the lung.
 A WT
Set9-
KO
Bleo
PBS mycin PBS
kD
200
116
97
66
45 Set9

31

TFIIB

Whole Lung Tissue

B Lung mRNA WT Set9-KO

Cdh1 HmgA2 Has2 Twist Snai1

9 7
1,2 6 8 3
6
Rel. mRNA levels

1 5 7
* 6 5 *
0,8 4 * 2
* 5 4
0,6 3 *
4 3
0,4 2 3 2 1
2
0,2 1 1 1

C Ble C Ble C Ble C Ble C Ble

C
Cdh1 HmgA2 Has2 Twist Snai1
1,2 5 3
5 3
1
Rel. mRNA levels

4 4
0,8 * * 2 *
3 * 2
0,6 3
* 2 2
0,4 1 1
0,2 1 1

C Ad C Ad C Ad C Ad C Ad
TGF-β TGF-β TGF-β TGF-β TGF-β

Figure S6 (Related to Figure 6)

(A) Set9 expression levels are not affected in bleomycin induced pulmonary fibrosis. Extracts from lung
tissues of untreated (PBS) and bleomycin-treated (Bleomycin) wild type (WT) and Set9-KO mice were
analyzed in western blots using antibodies against Set9 (upper panel) and TFIIB (lower panel).
(B) qPCR analysis of the mRNA levels of the indicated panel of genes involved in the regulation of
Epithelial-Mesenchymal Transition (Cdh1, HmgA2, Has2, Twist, Snai1) in the lungs of wild type (WT)
and Set9-KO mice after treatment with PBS (C) or bleomycin (Ble). Bars represent mean values of
mRNA levels normalized to Gapdh mRNA ± sem. Data are from triplicate measurements of total RNAs
from 4 individual mice. * p value < 0.05. (two-tailed Student’s t-test).
(C) qPCR analysis of lung mRNAs from mice treated with empty adenovirus vector (C) or with Ad-TGF-
β. Normalizations and statistical analysis was performed as in B.
Supplemental Experimental Procedures

Masson’s trichrome staining

Deparaffinized formalin-fixed lung tissues were rehydrated and incubated with Bouin’s solution (25 vol
37% formaldehyde, 70 vol saturated picric acid and 5 vol acetic acid) for 1 hr at 56 oC. After extensive
washing with H2O the sections were stained for 10 min with Wegert’s solution (0.5% Hematoxylin, 0.6%
Ferric chloride 50% ethanol and 0.5 v/v concentrated HCl). The sections were washed with H2O and
stained for 5 min with biebrich scarlet-acid fuchsin solution, made by mixing 90 ml 1% biebrich scarlet,
10 ml 1% acid fuchsin and 1 ml acetic acid. After washing with H2O the sections were incubated for 5
min with 1% phosphomolybdic / phosphotungstic Acid solution followed by washes and staining with
2.5% aniline-blue in 2% acetic acid for 10 minutes.

Measurements of lung mechanics

Mice were anesthetized with intra-peritoneal injection of 0.051 ml/10g bodyweight of a mixture of
ketamine (20 mg/ml, Merial SAS) and xylazine (1.3 mg/ml, Bayer AG). Once surgical anaesthesia had
been established the trachea was exposed, cannulated with a blunted metal 18-gauge needle and
connected to a computer-controlled small animal ventilator (FlexiVent, SCIREQ) (Apostolou et al.,
2012). The animals were placed on a 37°C heating pad to maintain body temperature during the
experiment and ventilated with a tidal volume of 8 ml/kg, at a normal respiratory rate (150
breaths/minute). A positive end-expiratory pressure of 0.2 kPa was established by placing the expiratory
line in a water trap. Each animal was paralyzed with intra-peritoneal injection of 0.05 ml/10g bodyweight
of rocuronium bromide (0.01 mg/ml, N.V. Organon) to suppress spontaneous breathing and allowed to
equilibrate on the ventilator. The lung volume history of the mice was standardized prior to measurement
of lung mechanics using three deep inflations at total lung capacity. Interference of the ventilator's
mechanical parts or the tracheal cannula to the measurements was eliminated using dynamic calibration
as previously described (Tomioka et al., 1985).

Mass spectrometry
Tryptic digestion of in vitro methylated proteins using 1 M cold S-Adenosyl-Methionine was performed
using the filter-aided sample preparation digestion protocol (Wisniewski et al., 2009). Proteins were
dissolved in a solution of 8M urea, 4% (w/v) SDS and 100mM Tris, pH 8.6 and added on top of a
centrifugal filtering unit with a 10 kDa molecular weight cut-off (Sartorius). Protein reduction, alkylation
and tryptic digestion were performed step by step in the centrifugal unit. After 16 hr digestion at 37°C,
peptides were eluted twice with 150 µL water and evaporated to dryness. Peptides were reconstituted in
2% acetonitrile/0.1% formic acid. 2 μg of dissolved peptides were pre-concentrated on a C18 trap column
and then separated on a 50-cm nano-column (75 μm ID, particle size 2 μm, 100Å, Acclaim PepMap
RSLC - Thermo Scientific) coupled via a nano-electrospray source to an LTQ Orbitrap XL (Thermo
Scientific) mass spectrometer. Peptides were separated with a linear gradient from 2% to 95% acetonitril
in 0.1% formic acid in 210 minutes. A mass spectrometric top6 method for data-dependent acquisition at
60K resolving power was used. Full scans (m/z range 300-2000) were acquired in the Orbitrap mass
spectrometer after accumulating up to 106 charges. The six most abundant and multiple charged
precursors were fragmented using collision-induced dissociation and their MS/MS spectra were acquired
in the ion trap. Dynamic exclusion was enabled for 90 sec.
Raw result files were analyzed using Thermo Scientific™ Proteome Discoverer™ software version 2.0
using SEQUEST HT (1.17). Peak lists were searched against the Uniprot mouse-specific database with
an initial mass deviation of 10 ppm, fragmentation mass deviation of 0.8 Da and trypsin digestion
specificity allowing up to two missed cleavages. Carbamidomethylation, oxidation of methionine, mono-,
di-, tri- methylation of lysine and acetylation of the protein N-terminus were used as variable
modifications. The peptides were filtered according to their XCorr score versus charge state and only
high confidence peptides were evaluated for their methylation status.
Antibodies
Mouse monoclonal anti-Smad7 (R&D Systems, #MAB2029), rabbit polyclonal anti-Smad7 (Life
Technologies, #42-0400), anti-GAPDH (Santa Cruz Biotechnology, sc-32233), anti-Set7/9 (Millipore,
#04-805), anti-TFIIB (Santa Cruz Biotechnology, sc-225), anti-Ubiquitin (Santa Cruz Biotechnology, sc-
8017), anti-HA-tag (Santa Cruz Biotechnology, sc-7392), anti-acetyl-lysine (Abcam, ab21623), anti-
RNF111 (Sigma, HPA038576), anti-Smurf1 (Cell Signaling, #2174), anti-Smurf2 (Cell Signaling,
#12024), anti-TGF-RI (Cell Signaling, #3712), anti-SMA (Sigma Aldrich #C6198), anti-CD45 (BD
Biosciences, #550539), anti-p53 (Abcam, ab1101).
Methylation-specific Smad7 antibody was raised in rabbits against the peptide Ac-
C(Ahx)AVRGAKme1GHH-amide, containing Ahx six-carbon spacer, by New England Peptide, that was
subjected to double affinity purification against methylated and non-methylated peptides. The specificity
of the antibody was verified by western blot analysis of in vitro methylated Smad7 proteins (Figure S3).

Primer sequences

The nucleotide sequences of primer sets used were the following:

Mouse Col4A2 NM_009932.3 5' GACCGAGTGCGGTTCAAAG 3'

5' CGCAGGGCACATCCAACTT 3'

Mouse Col7A1 NM_007738.3 5' GCCCAGAGATAGAGTGACCTG 3'

5' CGCACTTCTCGAAAGTTGCTG 3'

Mouse Ctgf NM_010217.2 5' GGGCCTCTTCTGCGATTTC 3'

5' ATCCAGGCAAGTGCATTGGTA 3'

Mouse Fbn1 NM_007993.2 5' GGACGCCAATTTGGAGGCT 3'

5' CTTTCAGCGCATCGTGTCCT 3'

Mouse Fn NM_010233.2 5' ATGTGGACCCCTCCTGATAGT 3'

5' GCCCAGTGATTTCAGCAAAGG 3'

Mouse Gapdh NM_008084 5' CCAATGTGTCCGTCGTGGATCT3'

5' GTTGAAGTCGCAGGAGACAACC 3'

Mouse Itg5A NM_010577.3 5' CTTCTCCGTGGAGTTTTACCG 3'

5' GCTGTCAAATTGAATGGTGGTG 3'

Mouse Krt16 NM_008470.1 5' CTCCAACAGCGAACTGGTACA 3'

5' CACACTGCCAATCAGTCCCT 3'

Mouse Krt17 NM_010663.2 5' GCCGCATCCTCAACGAGAT 3'

5' CGCGGTTCAGTTCCTCTGTC 3'

Mouse Serpine1 NM_008871.2 5' TCTGGGAAAGGGTTCACTTTACC 3'

5' GACACGCCATAGGGAGAGAAG 3'

Mouse Hmga2 NM_010441.2 5' CATTGGAGAAAAACGGCCAAG 3'

5' TTGCGAGGATGTCTCTTCAGT 3'

Mouse Has2 NM_008216.3 5' GTACGGTGCCTTTTTAGCCTC 3'

5' TAATCGGGGTTTCAAGGGACT 3'
Mouse Snai1 NM_011427.2 5' CCACACTGGTGAGAAGCCATTC 3'
5' GACATGCGGGAGAAGGTTCG 3'

Mouse Twist NM_011658.2 5' GCTACGCCTTCTCCGTCTG 3'

5' AATGACATCTAGGTCTCCGGC 3'

Mouse Cdh1 NM_009864.2 5’AGACCAGGACTTTGATTTGAGCCA 3’

5’CATCAGGATTGGCAGGACGG 3’

Human COL1A1 NM_011658.2 5' GATCTGCGTCTGCGACAAC3'

5' GGCAGTTCTTGGTCTCGTCA 3'

Human COL3A1 NM_000090.3 5' TTGAAGGAGGATGTTCCCATCT 3'

5' ACAGACACATATTTGGCATGGTT 3'

Human COL4A1 NM_001845.5 5' GGGATGCTGTTGAAAGGTGAA 3'

5' GGTGGTCCGGTAAATCCTGG 3'

Human COL4A2 NM_001846.2. 5' TTATGCACTGCCTAAAGAGGAGC 3'

5' CCCTTAACTCCGTAGAAACCAAG 3'

Human COL7A1 NM_000094.3 5' GCTGACATTGTGTTCTTACTGGA 3'

5' TCCGTGGGTCATCGCTGTA 3'

Human CTGF NM_001901.2 5' ACCGACTGGAAGACACGTTTG 3'

5' CCAGGTCAGCTTCGCAAGG 3'

Human FBN NM_000138.4 5' GCGGAAATCAGTGTATTGTCCC 3'

5' TGCAGTGTTGTATGGATCTGGA 3'

Human FN NM_212482.1 5' GAAGGCTTGAACCAACCTACG 3'

5' TGATTCAGACATTCGTTCCCAC 3'

Human GAPDH NM_002046.5 5' CCTCTGACTTCAACAGCGACAC 3'

5' AGCCAAATTCGTTGTCATACCAG 3'

Human ITG5A NM_002205.2 5' GCCTGTGGAGTACAAGTCCTT 3'

5' AATTCGGGTGAAGTTATCTGTGG 3'

Human KRT17 NM_000422.2 5' GCCGCATCCTCAACGAGAT 3'

5' CGCGGTTCAGTTCCTCTGTC 3'

Human SERPINE1 NM_000602.4 5' GCACCACAGACGCGATCTT 3'

5' ACCTCTGAAAAGTCCACTTGC 3'

Supplemental References

Tomioka, S., Bates, J. H., and Irvin, C. G. (2002). Airway and tissue mechanics in a murine model of
asthma: alveolar capsule vs. forced oscillations. J. Appl. Physiol. 93, 263-270.

Wisniewski, J. R., Zougman, A., Nagaraj, N., and Mann, M. (2009). Universal sample preparation
method for proteome analysis. Nat. Methods 6, 359-362.