A

0

1

2

3

4** **

Tubu

lar d

amag

e sc

ore

(AU

)

B6

Sh

FVB B6

Nx

FVB

B6 FVB

Sh

Nx

C ShB6 ShFVB NxFVBNxB6

Day

2D

ay 2

8D

ay 5

6

KI6

7

B

Supplemental Figure 1. Tubular injury and cell proliferation after nephron reduction. (A) Representative imagesstained with PAS (left panels, original magnification, X400) and quantification (right panel) of tubular lesions in FVB andB6 mice 2 days after sham-operation (Sh) or subtotal nephrectomy (Nx). n = 4-6 and n = 10-12 for Sh and Nx,respectively in each strain. Data are means ± SEM. ANOVA was followed by the Tukey–Kramer test. Nx versus Shmice: ** P <0.01. (B) mRNA expression of Lcn2 in FVB and B6 mice 2 days after Sh or Nx (n = 5-6 and n = 10 for Shand Nx, respectively in each strain). Data are means ± SEM. ANOVA was followed by the Tukey–Kramer test. Nxversus Sh mice: ** P < 0.01, *** P < 0.001. (C) Representative cortical sections from FVB and B6 mice 2, 28, and 56days after Sh or Nx stained with anti- KI-67 antibody (original magnification, X200; n = 4-6 and n = 10-12 for Sh andNx, respectively in each strain at each time point).

0

20

40

60

80

100

**

***

Rel

ativ

e m

RN

A qu

antit

y (fo

ld)

B6

Sh

FVB B6

Nx

FVB

Lcn2

B6

Sh

FVB B6

Nx

FVB B6

Sh

FVB B6

Nx

FVB B6

Sh

FVB B6

Nx

FVB

Day 56Day 28Day 2

10

15

20

25

30

*

**### ###

Body

wei

ght (

g)

10

15

20

25

30

******

### ###

Body

wei

ght (

g)

10

15

20

25

30## ###

Body

wei

ght (

g)

A

B6

Sh

FVB B6

Nx

FVB B6

Sh

FVB B6

Nx

FVB B6

Sh

FVB B6

Nx

FVB

Day 56Day 28Day 2

0

100

200

300

400

*** **

Kidn

ey w

eigh

t (m

g)

0

100

200

300

400

** *#

Kidn

ey w

eigh

t (m

g)

0

100

200

300

400 ###***

Kidn

ey w

eigh

t (m

g)

B

Supplemental Figure 2. Time-course analysis of body and kidney weight. (A) Body weight and (B) kidney weightin B6 and FVB mice 2, 28, and 56 days after sham-operation (Sh) or subtotal nephrectomy (Nx). n = 4-6 and n = 9-12for Sh and Nx, respectively in each strain at each time point. Data are means ± SEM. ANOVA was followed by theTukey–Kramer test. Nx versus Sh mice: * P < 0.05, ** P < 0.01, ***P < 0.001; FVB versus B6 mice: # P < 0.05, ## P <0.01, ### P < 0.001.

A

B

C

Supplemental Figure 3. Time-course quantification of renal lesions. (A) Glomerular lesions score, (B) tubular

dilatation area and (C) fibrosis score of kidneys from FVB and B6 mice 2, 28, and 56 days after sham-operation (Sh) or

subtotal nephrectomy (Nx). n = 4 and 6 for Sh and Nx, respectively in each strain at each time point. Data are means ±SEM. ANOVA was followed by the Tukey–Kramer test. Nx versus Sh mice: * P < 0.05, ** P < 0.01, *** P < 0.001; FVB

versus B6 mice: # P < 0.05, ### P < 0.001.

B6

Sh

FVB B6

Nx

FVB

Day 2

0

10

20

30

40

50###

Tubu

lar d

ilatio

n ar

ea (%

)

B6

Sh

FVB B6

Nx

FVB

Day 28

0

10

20

30

40

50###

Tubu

lar d

ilatio

n ar

ea (%

)

B6

Sh

FVB B6

Nx

FVB

Day 56

0

10

20

30

40

50 ***###

Tubu

lar d

ilatio

n ar

ea (%

)

B6

Sh

FVB B6

Nx

FVB

Day 2

0

5

10

15

20

Fibr

osis

(%)

B6

Sh

FVB B6

Nx

FVB

Day 56

0

5

10

15

20***

###

***

Fibr

osis

(%)

B6

Sh

FVB B6

Nx

FVB

Day 28

0

5

10

15

20

***

***#

Fibr

osis

(%)

B6

Sh

FVB B6

Nx

FVB

Day 2

0

1

2

3

4

** **

Glo

mer

ular

lesi

ons

scor

e (A

U)

B6

Sh

FVB B6

Nx

FVB

Day 28

0

1

2

3

4

***

Glo

mer

ular

lesi

ons

scor

e (A

U)

B6

Sh

FVB B6

Nx

FVB

Day 56

0

1

2

3

4

*

***###

Glo

mer

ular

lesi

ons

scor

e (A

U)

B6

Sh

FVB B6

Nx

FVB B6

Sh

FVB B6

Nx

FVB B6

Sh

FVB B6

Nx

FVB0

10

20

30

40

50***#

Seru

m C

reat

inin

e (µ

mol

.l-1)

Day 56Day 56Day 56

0

5

10

15

20***###

Urin

e Pr

ot/C

reat

(mg/

mm

ol)

0510

1500

3000

4500

6000###***

Urin

e Al

b/Cr

eat (

mg/

mm

ol)

Supplemental Figure 4. Renal function. Serum creatinine, urine protein-to-creatinine ratio and urine albumin-to-creatinine ratio in FVB and B6 mice 56 days after sham-operation (Sh) or subtotal nephrectomy (Nx). n = 6 and n = 9-11 for Sh and Nx, respectively in each strain. Data are means ± SEM. ANOVA was followed by the Tukey–Kramer test.Nx versus Sh mice: *** P < 0.001; FVB versus B6 mice: # P < 0.05, ### P < 0.001.

Sh

B6 FVB

Nx

Supplemental Figure 5. Cell proliferation interests mainly tubular cells. Representative images of co-localizationexperiments using anti-PCNA (blue) and anti-α-SMA antibodies in B6 and FVB mice 56 days after sham-operation (Sh)or subtotal nephrectomy (Nx). Original magnification, X200; n = 6 both Sh and Nx in each strain.

PCNAα-SMA

Technical quality control

Statistical model

Unbiased analysis

Geneset enrichment analysis (GSEA)

2days

56days

28days

mRNA(n=48)

Compensatoryphase

Deteriorationphase

Quiescent phase

B6

FVB

Surgery

n=4/each time

Supplemental Figure 6. Experimental protocol used for transcriptomic analysis. Four mice per group (sham-operation, Sh; or subtotal nephrectomy, Nx) of each strain (B6 and FVB) at each time point (2, 28, and 56 days aftersurgery, corresponding to the renal compensatory, quiescent, and deterioration phases, respectively) were used forwhole-kidney transcriptomic analysis. Overall, microarray analysis was performed on 48 mice. A full statistical modelwas fitted to the expression data in order to consider: (1) the strain (FVB versus B6), (2) the surgery (Nx versus Sh),and (3) the time after surgery (2 versus 28 versus 56 days) effect. Unbiased clustering analysis was performed usingco-inertia analysis. Gene-set enrichment analysis was then performed using a collection of gene signatures from PID,Pathway Commons and Reactome.

Isg15

0

2

4

6

8

10***

Rel

ativ

e m

RN

A qu

antit

y (A

U)

Day 2

ShFVB NxFVB0

2

4

6

8

10

Rel

ativ

e m

RN

A qu

antit

y (A

U)

Day 56

ShFVB NxFVB0

2

4

6

8

10

Rel

ativ

e m

RN

A qu

antit

y (A

U)

Day 28

ShFVB NxFVB

Usp18

0

1

2

3

4

5***

Rel

ativ

e m

RN

A qu

antit

y (A

U)

Day 2

ShFVB NxFVB0

1

2

3

4

5

Rel

ativ

e m

RN

A qu

antit

y (A

U)

Day 56

ShFVB NxFVB0

1

2

3

4

5

Rel

ativ

e m

RN

A qu

antit

y (A

U)

Day 28

ShFVB NxFVB

Irf7

0

2

4

6***

Rel

ativ

e m

RN

A qu

antit

y (A

U)

Day 2

ShFVB NxFVB0

2

4

6

*

Rel

ativ

e m

RN

A qu

antit

y (A

U)

Day 56

ShFVB NxFVB0

2

4

6

*

Rel

ativ

e m

RN

A qu

antit

y (A

U)

Day 28

ShFVB NxFVB

Ifi202b

0

500

1000

1500

2000 ***

Rel

ativ

e m

RN

A qu

antit

y (A

U)

Day 2

ShFVB NxFVB0

500

1000

1500

2000

***

Rel

ativ

e m

RN

A qu

antit

y (A

U)

Day 56

ShFVB NxFVB0

500

1000

1500

2000

**

Rel

ativ

e m

RN

A qu

antit

y (A

U)

ShFVB NxFVB

Day 28

Ifi204

0

2

4

6

8

10***

Rel

ativ

e m

RN

A qu

antit

y (A

U)

Day 2

ShFVB NxFVB0

2

4

6

8

10

**

Rel

ativ

e m

RN

A qu

antit

y (A

U)

Day 56

ShFVB NxFVB0

2

4

6

8

10

**

Rel

ativ

e m

RN

A qu

antit

y (A

U)

ShFVB NxFVB

Day 28

Supplemental Figure 7. Time-course analysis of type I IFN induced genes expression after nephron reduction.mRNA expression of Ifi202b, Ifi204, Isg15, Usp18, and Irf7 in FVB mice 2, 28, and 56 days after sham-operation (Sh)or subtotal nephrectomy (Nx). n = 4-6 and n = 9-11 for Sh and Nx, respectively in each strain at each time point. Dataare means ± SEM. Mann Withney test. Nx versus Sh mice: * P < 0.05, ** P <0.01, *** P <0.001.

0

1

2

3

4

***

***

***

***

***

***

Rel

ativ

e m

RN

A qu

antit

y (A

U)

Irf7

Sh

Day 7

CK OK Sh

Day 14

CK OK Sh

Day 21

CK OK

Ifi204

Sh

Day 7

RK LK Sh

Day 14

RK LK Sh

Day 21

RK LK0

1

2

3

4

***

***

***

***

***

***R

elat

ive

mR

NA

quan

tity

(AU

)

Ifi205

Sh

Day 7

RK LK Sh

Day 14

RK LK Sh

Day 21

RK LK0

1

2

3

4

*

*

*

*

*

*

Rel

ativ

e m

RN

A qu

antit

y (A

U)

Isg15

Sh

Day 7

CK OK Sh

Day 14

CK OK Sh

Day 21

CK OK0

1

2

3

4

*

**

*

**

*

**

Rel

ativ

e m

RN

A qu

antit

y (A

U)

Usp18

Sh

Day 7

CK OK Sh

Day 14

CK OK Sh

Day 21

CK OK0

1

2

3

4

***

***

***

***

***

***

Rel

ativ

e m

RN

A qu

antit

y (A

U)

Supplemental Figure 8. Unilateral ureteral obstruction results in early type I IFN response. mRNA expression ofIfi204, Ifi205, Isg15, Usp18 and Irf7 in B6 mice 7, 14, and 21 days after sham-operation (Sh) or unilateral ureteralobstruction (UUO) in non obstructed control kidney (CK) and obstructed kidney (OK). n = 3-4 and n = 5-6 for Sh andUUO, respectively at each time-point. Data are means ± SEM. ANOVA was followed by the Tukey–Kramer test. OKversus Sh or CK: * P < 0.05, ** P < 0.01, *** P < 0.001.

B6

Sh

FVB B6

Nx

FVB B6

Sh

FVB B6

Nx

FVB

Day 56Day 28A

B6

Sh

FVB B6

Nx

FVB

Day 2

0.0

0.2

0.4

0.6

***##

CD

3+ c

ells

/ fie

ld (%

)

0.0

0.2

0.4

0.6 **

CD

3+ c

ells

/ fie

ld (%

)

0.0

0.2

0.4

0.6 *

*

CD

3+ c

ells

/ fie

ld (%

)

B6

Sh

FVB B6

Nx

FVB B6

Sh

FVB B6

Nx

FVB

Day 56Day 28B

B6

Sh

FVB B6

Nx

FVB

Day 2

0.0

0.5

1.0

1.5

2.0

***

F4/8

0+ c

ells

/ fie

ld (%

)

0.0

0.5

1.0

1.5

2.0

F4/8

0+ c

ells

/ fie

ld (%

)

0.0

0.5

1.0

1.5

2.0 **

*

F4/8

0+ c

ells

/ fie

ld (%

)

Supplemental Figure 9. Time-course quantification of renal inflammatory cell infiltration. (A) Quantification of T-lymphocytes and (B) monocytes-macrophages in B6 and FVB mice 2, 28, and 56 days after sham-operation (Sh) orsubtotal nephrectomy (Nx) by CD3 and F4/80 immunohistochemistry, respectively. n = 4 for both Sh and Nx, in eachstrain at each time point. Data are means ± SEM. ANOVA was followed by the Tukey–Kramer test. Nx versus Sh mice:* P < 0.05, ** P < 0.01, *** P < 0.001; FVB versus B6 mice: ## P < 0.01.

Gene Primer Sequence (5’- - - - - 3’)

Cdkn1a F GGAACATCTCAGGGCCGAAAR CTGACCCACAGCAGAAGAGG

Ifi202b F ATTCCAGCGTGTCTGAGGTGR ACCACCACTTTCATTGCTCCT

Ifi204 F TAGAAGTGGTGGGGAGTGGAR GCACCATCACTTGTTTGGGAC

Ifi205 F TTGTGAACGTGTACCAACTCTR TGCCTTGATCTTCTTCACGTC

Isg15 F TCTGACTGTGAGAGCAAGCAR ACCAGGAAATCGTTACCCCC

Usp18 F AAGGACGCAAAGCCTCTGAAR ATGGTCAAGGTTTGGGGCAG

Irf7 F GTCACCACACTACACCATCTACR CCATGAGGAAGTGTTCGATGT

Cd3 F AAGCCTGTGACCCGAGGAAR TGCGGATGGGCTCATAGTCT

Mac1 F CTTCCAGGGCAGGAGTCGTATR CAATGGAGCTGCCCACAAT

SiglecH F CAGAACTCCACAGCCCATGTR TGTGTTGCTGGTCTCTCCAC

Tlr7 F GTTCTTGACCTTGGCACTR CCGTGCATATTCATCGTA

Kim1 F GAGAGTGACAGTGGTCTGTATTGR CCTTGTAGTTGTGGGTCTTCTT

Lcn2 F GGACCAGGGCTGTCGCTACTR GGTGGCCACTTGCACATTGT

Ripk3 F GCCTTCCTCTCAGTCCACACR ACGCACCAGTAGGCCATAAC

Mlkl F AGGATGCAGAGGAAGACGGAR TGGGATCTCCTGTGTGGGTT

Rpl13 F CTCATCCTGTTCCCCAGGAAR GGGTGGCCAGCTTAAGTTCTT

Supplemental Table 1: Primers used in the study.