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Supplemental Figure Legends Supplemental Figure 1. Western blot analysis indicated that was detected in the fractions of plasma membrane and cytosol but not in nuclear fraction isolated from Pkd1 null MEK cells. The isolation (fractionation) of plasma membrane, cytosol and nuclear was described in Methods section. Na/K-ATPase, -tubulin and lamin A/C were used as markers for membrane, cytosol and nuclear, respectively. Supplemental Figure 2. Treatment with ISO-1 delayed cyst growth in Pkd1 flox/flox :Ksp-Cre neonates. (A) Histologic examination of PN7 kidneys from Pkd1 flox/flox :Ksp-Cre neonates treated with vehicle (DMSO) (n = 1) or ISO-1 (n = 6), respectively. Scale bar, 1 mm. (B) Quantification of the percentage of cystic areas over total kidney section areas of PN7 kidney sections from Pkd1 flox/flox :Ksp-Cre neonates treated as in A. Shown is mean ± s.e.m. of all sections quantified for each condition. p <.1. (C and D) KW/BW ratios (C) and BUN levels (D) were decreased in Pkd1 flox/flox :Ksp-Cre PN7 neonates treated with ISO-1 compared to that treated with DMSO (control). p <.1. (E) ISO-1 treatment reduced cyst lining epithelial cell proliferation in Pkd1 flox/flox :Ksp-Cre PN7 kidneys as detected by Ki67 staining. p <.1. Scale bar, 1 µm. (F) ISO-1 treatment induced cyst lining epithelial cell apoptosis in Pkd1 flox/flox :Ksp-Cre PN7 kidneys as detected by TUNEL assay. p <.1. Scale bar, 1 µm. Supplemental Figure 3. Statistical analysis of the body weight of Pkd1 flox/flox :Ksp-Cre mice at postnatal day 7, Pkd1 flox/flox :Pkhd1-Cre mice at postnatal day 25 and Pkd1 nl/nl mice at postnatal day 28 treated with DMSO and ISO-1 respectively. Supplemental Figure 4. Western blot analysis of in two kidneys from Pkd1 flox/flox :Ksp-Cre:, Pkd1 +/+ :Ksp-Cre: and Pkd1 flox/flox :Ksp-Cre: neonates, respectively. 1

Supplemental Figure 5. Knockout of or inhibition of with ISO-1 leads to diminished levels of macrophages in pericystic and interstitial regions of Pkd1 conditional knockout mouse kidneys. (A) The accumulation/recruitment of macrophages to pericystic sites and interstitium in kidneys from Pkd1 flox/flox :Ksp-Cre: mice was dramatically reduced at postnatal day 7 compared to that from age matched kidneys of Pkd1 flox/flox :Ksp-Cre: mice. p <.1. Scale bar, 1 µm. (B-D) Treatment with ISO-1 dramatically reduced the accumulation/recruitment of macrophages to pericystic sites and interstitium in kidneys from Pkd1 flox/flox :Ksp-Cre mice at postnatal day 7 (B), Pkd1 flox/flox :Pkhd1-Cre mice at postnatal day 25 (C) and Pkd1 nl/nl mice at postnatal day 28 (D) compared to that from age matched kidneys of Pkd1 flox/flox :Ksp-Cre mice, Pkd1 flox/flox :Pkhd1-Cre mice and Pkd1 nl/nl mice treated with DMSO, respectively. p <.1. Scale bar, 1 µm. Supplemental Figure 6. Treatment with ISO-1 decreased the expression of in Pkd1 mutant kidneys from Pkd1 flox/flox :Ksp-Cre mice and Pkd1 flox/flox :Pkhd1-Cre mice compared to that from age matched control mice treated with DMSO. (A and B) Western blot analysis of the expression of in kidneys from three different Pkd1 flox/flox :Ksp-Cre mice (A) and Pkd1 flox/flox :Pkhd1-Cre mice (B) treated with DMSO or ISO-1, respectively. (C and D) Immunohistochemistry staining of in kidneys from Pkd1 flox/flox :Ksp-Cre mice (C) and Pkd1 flox/flox :Pkhd1-Cre mice (D) treated with DMSO or ISO-1, respectively. Scale bar, 1 µm. Supplemental Figure 7. can be secreted in cell culture media of renal epithelial cells and is highly enriched in cyst fluids and urines derived from two distinct orthologous mouse models of ADPKD. (A) Western blot analysis of the levels of in cell culture media of Pkd1 wild type (WT) and mutant (Null) MEK cells standardized to the same cell numbers of different cell types. p <.1. (B) Western blot analysis of the levels of in cyst fluids from four different Pkd1 flox/flox :Ksp-Cre mice and 2

Pkd1 flox/flox :Pkhd1-Cre mice, respectively. (C) Western blot analysis of the levels of in urines from Pkd1 flox/flox :Ksp-Cre mice at PN7 and PN14 as well as from Pkd1 flox/flox :Pkhd1-Cre mice at PN14 and PN25, respectively. Supplemental Figure 8. (A) Western blot analysis of the levels of in cyst fluids from five male and five female ADPKD patients, respectively. Our results indicated that might form a dimer in human cyst fluids. (B) Western blot analysis of the levels of in urines from four male ADPKD patients and four normal males (top panel) as well as from four female patients and four normal females (bottom panel), respectively. Supplemental Figure 9. promotes macrophage migration. Addition of ISO-1 (1 µm) blocked ADPKD CM-induced migration of human THP-1 monocytes. p <.1; ANOVA post hoc test. Supplemental Figure 1. (A) MCP-1 expression was increased in Pkd1 mutant mouse embryonic kidney (MEK) cells and postnatal Pkd1 homozygous PN24 cells compared to Pkd1 wild-type MEK cells and postnatal Pkd1 heterzygous PH2 cells as analyzed with western blot. (B-D) MCP-1 was elevated in kidneys from Pkd1 flox/flox :Ksp-Cre mice (B) and Pkd1 flox/flox :Pkhd1-Cre mice (C) as well as in kidneys from ADPKD patients (D) compared to that in age matched wild type mouse kidneys and normal human kidneys as analyzed with immunohistochemistry staining, respectively. Treatment with ISO-1 decreased the expression of MCP-1 in Pkd1 mutant kidneys from Pkd1 flox/flox :Ksp-Cre mice (B) and Pkd1 flox/flox :Pkhd1-Cre mice (C) compared to that in age matched control kidneys treated with DMSO, respectively. Supplemental Figure 11. Treatment with ISO-1 decreased the levels of MCP-1 mrna (A) and protein (B) in kidneys from Pkd1 flox/flox :Pkhd1-Cre mice compared with DMSO treated control mice as examined by qrt-pcr and western blot, respectively. n = 3, p <.5; ANOVA post hoc test. 3

Supplemental Figure 12. promotes the expression of MCP-1 and TNF- whereas TNF- also induces the expression of in renal epithelial cells. (A and B) Western blot analysis of the expression of MCP-1 and TNF- from whole cell lysates of Pkd1 mutant PN24 cells (A) and Pkd1 mutant MEK cells (B) induced with (1 ng/ml) at indicated time points. C. Western blot analysis of the expression of from whole cell lysates of Pkd1 wild type and null MEK cells induced with TNF- (5 ng/ml) at indicated time points. Supplemental Figure 13. (A and B) qrt-pcr analysis of the expression of Hk1 (A) and Ldha (B) mrna in Pkd1 wild type (WT) and mutant (Null) MEK cells untreated or treated with ISO-1 or sirna. The transcription of the key glycolytic enzymes, Hk1 and Ldha (p <.1; ANOVA post hoc test.) was significantly increased in Pkd1 mutant (Null) MEK cells compared to Pkd1 wild type MEK cells. Treatment with ISO-1 or sirna did not affect the transcription of the key glycolytic enzymes, Hk1 and Ldha, in Pkd1 wild type MEK cells. However, treatment with ISO-1 or sirna significantly decreased the transcription of Hk1 and Ldha (p <.1; ANOVA post hoc test.) in Pkd1 mutant (Null) MEK cells compared to untreated Pkd1 mutant (Null) MEK cells, respectively. Supplemental Figure 14. (A) Western blot analysis of the expression of ERK and phospho-erk from whole cell lysates of Pkd1 mutant PN24 cells treated with (1 ng/ml) or ISO-1 (1 M) at indicated time points. (B) Western blot analysis of the levels of phospho-erk in Pkd1 null cells and PN24 cells treated with conditional media collected from Pkd1 null MEK cells transfected with control sirna or sirna for 72 hours. The phosphorylation of ERK could be induced in Pkd1 null cells and PN24 cells treated with conditional media collected from cystic renal epithelial cells transfected with control sirna at indicated time points but could not be induced in these cells treated with conditional media collected from knockdown cystic renal epithelial cells. 4

Supplemental Figure 15. Western blot analysis of the expression of from whole cell lysates of Pkd1 mutant (Null) MEK cells treated with Hsp9 inhibitors, STA99 (1 nm) or 17-AAG (1 µm), at indicated time points. Supplemental Figure 16. (A-B) Analysis of the expression of CD74 protein (A) and mrna (B) of Pkd1 wild-type (WT) and Pkd1 null/null (Null) MEK cells as well as postnatal Pkd1 heterozygous PH2 (PH2) cells and Pkd1 homozygous PN24 (PN24) cells by Western blot and qrt-pcr, respectively. (C) CD74 was elevated in kidney sections from normal and ADPKD kidneys as examined by immunohistochemistry staining with anti-cd74 antibody. Scale bar, 1 µm. (D) Western blot analysis of the expression of phospho-erk, total ERK and MCP-1 in PN24 cells that were pretreated with normal IgG or CD74 antibody for 2 hours and then were stimulated with recombinant (1 ng/ml) at indicated time points. Treatment with CD74 antibody blocked induced the phosphorylation of ERK but did not affect induced MCP-1 expression. 5

Supplemental Figure 1 Na/K-ATPase (membrane marker) a-tubulin (cytosol marker) Lamin A/C (nuclear Marker)

Cystic index (%) KW/BW ratio (%) Ki67 positive cells TUNEL-positive cells (%) BUN (mg/dl) Supplemental Figure 2 A DMSO ISO-1 B C D 8 1 15 6 4 2 1 mm E 8 p.1 6 4 2 1 p.1 p.1 5 DMSO ISO-1 DMSO ISO-1 DMSO ISO-1 25 2 15 1 p.1 5 F DMSO ISO-1 8 6 DMSO ISO-1 p.1 4 2 DMSO ISO-1 DMSO ISO-1

Body weight (g) Body weight (g) Body weight (g) Supplemental Figure 3 A 5 4 3 2 1 B 1 p =.24 8 p =.73 6 4 2 C 12 1 8 6 4 2 p =.64 DMSO ISO-1 Pkd1 flox/flox :Ksp-cre DMSO ISO-1 Pkd1 flox/flox :Pkhd1-cre DMSO ISO-1 Pkd1 nl/nl

Supplemental Figure 4 1 2 1 2 1 2

F4/8 positive cells per high power field F4/8 positive cells per high power field Supplemental Figure 5 A 25 2 15 1 p <.1 5 B Pkd1 flox/flox :Ksp-Cre: +/+ Pkd1 flox/flox :Ksp-Cre: -/- +/+ -/- 25 2 15 1 p.1 5 Pkd1 flox/flox :Ksp-cre + DMSO Pkd1 flox/flox :Ksp-cre + ISO-1 DMSO ISO-1

F4/8 positive cells per high power field F4/8 positive cells per high power field Supplemental Figure 5 C 25 2 15 1 p.1 5 DMSO ISO-1 Pkd1 flox/flox :Pkhd1-cre + DMSO Pkd1 flox/flox :Pkhd1-cre + ISO-1 D 25 2 15 1 p <.1 5 DMSO ISO-1 Pkd1 nl/nl + DMSO Pkd1 nl/nl + ISO-1

Supplemental Figure 6 A Pkd1 flox/flox :Ksp-cre, PN7 B Pkd1 flox/flox :Pkhd1-cre, PN25 ISO-1 - - - + + + ISO-1 - - - + + + C Pkd1 +/+ :Ksp-Cre Pkd1 flox/flox :Ksp-Cre + DMSO Pkd1 flox/flox :Ksp-Cre + ISO-1 D Pkd1 +/+ :Pkhd1-Cre Pkd1 flox/flox :Pkhd1-Cre + DMSO Pkd1 flox/flox :Pkhd1-Cre + ISO-1

Relative level in medium Supplemental Figure 7 A 4 p.1 WT null 3 2 1 WT null B Pkd1 flox/flox :Ksp-Cre Pkd1 flox/flox :Pkhd1-Cre 1 2 3 4 1 2 3 4 C PN7 PN14 WT Pkd1 flox/flox :Ksp-Cre WT Pkd1 flox/flox :Ksp-Cre PN14 PN25 WT Pkd1 flox/flox :Pkhd1-Cre WT Pkd1 flox/flox :Pkhd1-Cre

A Cyst fluids of ADPKD males Cyst fluids of ADPKD females Supplemental Figure 8 1 2 3 4 5 1 2 3 4 5 25 KD 12.5 KD B Urines of ADPKD patients Urines of normal humans 25 KD 1 2 3 4 1 2 3 4 12.5 KD (male) GFR BUN Age 16 35 77 77 47 3 17 11 51 44 46 41 25 KD 12.5 KD (female) GFR BUN Age 12 24 4 > 6 49 36 22 12 57 48 62 4

Fluorescence units Supplemental Figure 9 p <.1 ISO-1 in insert

Supplemental Figure 1 A WT Null MCP-1 D PH2 PN24 MCP-1 Normal kidney ADPKD kidney B Pkd1 +/+ :Ksp-Cre Pkd1 flox/flox :Ksp-Cre + DMSO Pkd1 flox/flox :Ksp-Cre + ISO-1 C Pkd1 +/+ :Pkhd1-Cre Pkd1 flox/flox :Pkhd1-Cre + DMSO Pkd1 flox/flox :Pkhd1-Cre + ISO-1

MCP-1 mrna Supplemental Figure 11 A 4 3 2 1 p<.1 p<.5 B Pkd1-WT ISO-1 - - - Pkd1 flox/flox :Pkhd1-cre, PN25 - - - + + + MCP-1 WT DMSO ISO-1 Pkd1 flox/flox :Pkhd1-cre

Supplemental Figure 12 A Null 1 3 2h MCP-1 TNF-a B PN24 1 3 2h MCP-1 TNF-a C TNFa WT h 6h 12h 24h Null

Hk1 mrna Ldha mrna Supplemental Figure 13 A 2.5 p<.1 p<.1 B 2.5 p<.1 p<.1 2 2 1.5 1.5 1.5 1.5

Supplemental Figure 14 A ISO-1 1 3 2h 3 2h 4h 12h 24h p-erk Total ERK B si-control conditional media si- conditional media 1 3 2h 1 3 2h p-erk Null-MEK Total ERK 1 3 2h 1 3 2h PN24 p-erk Total ERK

Supplemental Figure 15 STA-99 h 1h 2h 4h 17-AAG h 1h 2h 4h

CD74 mrna Supplemental Figure 16 A WT Null PH2 PN24 C CD74 Normal kidney ADPKD kidney B 4 3 2 1 p<.5 5 4 3 2 1 p<.1 D Normal IgG CD74 Ab 1 3 2h 1 3 2h p-erk Total ERK WT Null PH2 PN24 MCP-1

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