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A High-Throughput Screen Identifies DYRK1A Inhibitor ID-8 that Stimulates Human Kidney Tubular Epithelial Cell Proliferation

Maria B. Monteiro,1 Susanne Ramm,1,2 Vidya Chandrasekaran,1 Sarah A. Boswell,1 Elijah J. Weber,3 Kevin A. Lidberg,3 Edward J. Kelly,3 and Vishal S. Vaidya1,2,4

1Harvard Program in Therapeutic Science, Harvard Medical School Laboratory of Systems Pharmacology, Boston, Massachusetts; 2Renal Division, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts; 3Department of Pharmaceutics, University of Washington, Seattle, Washington; and 4Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts

ABSTRACT Background The death of epithelial cells in the proximal tubules is thought to be the primary cause of AKI, but epithelial cells that survive kidney injury have a remarkable ability to proliferate. Because proximal tubular epithelial cells play a predominant role in kidney regeneration after damage, a potential approach to treat AKI is to discover regenerative therapeutics capable of stimulating proliferation of these cells. Methods We conducted a high-throughput phenotypic screen using 1902 biologically active compounds to identify new molecules that promote proliferation of primary human proximal tubular epithelial cells in vitro. Results The primary screen identified 129 compounds that stimulated tubular epithelial cell proliferation. A secondary screen against these compounds over a range of four doses confirmed that eight resulted in a significant increase in cell number and incorporation of the modified thymidine analog EdU (indicating actively proliferating cells), compared with control conditions. These eight compounds also stimulated tubular cell proliferation in vitro after damage induced by hypoxia, cadmium chloride, cyclosporin A, or polymyxin B. ID-8, an inhibitor of dual-specificity tyrosine-phosphorylation-regulated kinase 1A (DYRK1A), was the top candidate identified as having a robust proproliferative effect in two-dimensional culture models as well as a microphysiologic, three-dimensional cell culture system. Target engagement and genetic knockdown studies and RNA sequencing confirmed binding of ID-8 to DYRK1A and upregulation of cyclins and other cell cycle regulators, leading to epithelial cell proliferation. Conclusions We have identified a potential first-in-class compound that stimulates human kidney tubular epithelial cell proliferation after acute damage in vitro.

J Am Soc Nephrol 29: 2820–2833, 2018. doi: https://doi.org/10.1681/ASN.2018040392

AKI affects one in five hospitalized patients world- the surviving epithelial cells are responsible for wide and its incidence is currently increasing.1,2 repopulating the tubule through a process of AKI is associated with substantial morbidity and mortality and is recognized as a leading cause of Received April 16, 2018. Accepted September 20, 2018. 3,4 CKD. M.B.M. and S.R. contributed equally to this work. The death of epithelial cells in the proximal tu- Published online ahead of print. Publication date available at 5 bules is thought to be the primary cause of AKI www.jasn.org. as these cells serve as sensors, effectors, and targets Correspondence: Dr. Vishal S. Vaidya, Harvard Institutes of 6 of injury. However, they also have a remarkable Medicine, Room 562, 77 Avenue Louis Pasteur, Boston, MA ability to proliferate and repair tubules after dam- 02115. Email: [email protected] age. During tissue repair after kidney injury, Copyright © 2018 by the American Society of Nephrology

2820 ISSN : 1046-6673/2912-2820 JAmSocNephrol29: 2820–2833, 2018 www.jasn.org BASIC RESEARCH dedifferentiation, proliferation, and redifferentiation.7 Re- Significance Statement cent evidence also shows that the AKI-to-CKD transition is triggered by the incomplete repair of the renal tubules after One potential therapeutic strategy for treating AKI, apart from injury, which may eventually lead to interstitial renal fibrosis.8 supportive care, dialysis, and transplantation, is stimulating the Therefore, we hypothesized that discovery of new therapeu- proliferation of proximal tubular epithelial cells. The authors de- fi scribe use of high-throughput screening to identify ID-8, an inhibitor tics that promote ef cient tubular epithelial cell proliferation of dual-specificity tyrosine-phosphorylation-regulated kinase 1A may allow regression of kidney injury, thereby preventing (DYRK1A), as a first-in-class compound that stimulates kidney tu- AKI and the development of fibrosis, and halting progression bular epithelial cell proliferation after different types of acute to CKD. damage in two- and three-dimensional in vitro models. They also in vitro In vitro phenotypic high-throughput screens (HTS) have provide evidence that ID-8 is able to bind DYRK1A in primary human proximal tubular epithelial cells and stimulate proliferation enabled the discovery of mitogenic small-molecule drugs that after injury by upregulating cell cycle mediators. This early-stage promote proliferation of pancreatic b cells and hepatocytes as discovery study identifies ID-8 as a potential therapeutic candidate potential therapeutics for diabetes and liver disease.9,10 We to stimulate regeneration and repair of epithelial cells in the kidney therefore conducted HTS to identify compounds that can after acute damage. stimulate kidney tubular epithelial cell proliferation. Primary human proximal tubular epithelial cells (HPTECs) have pre- (full medium, see Supplemental Material for a detailed de- in vitro viously been characterized as a relevant model scription). On day 1, full medium was replaced with for studying kidney cell damage and recovery in both two- DMEM/Ham-F12 GlutaMAX medium containing only peni- dimensional (2D) culture models and a three-dimensional (3D) cillin/streptomycin (free medium) to deprive cells of growth 11 in vitro microphysiologic system (MPS). These systems retain signals and increase their sensitivity to proliferative stimuli. many features of the differentiated kidney proximal tubular On day 3, cells were treated in duplicates with 11 mM dilutions epithelium, such as polar architecture; junctional assembly; of the Selleck library or with a panel of controls—full medium expression and activity of transporters; the ability to respond (positive control), free medium (negative control), or 0.1 mM to physiologic stimuli, stress, and toxicity; and the ability to digoxin (toxic control)—using a Seiko Compound Transfer 11,12 perform critical biochemical synthetic activities. We Robot. The 11 mM concentration was on the basis of previous screened primary HPTECs against the Selleck Bioactive Com- studies that performed similar assays.9,14,15 After treatment, pound Library, which contains structurally diverse, medici- live-cell imaging was performed using digital phase contrast to nally active, and cell-permeable FDA-approved compounds, generate a baseline cell count at 0 hour. On day 5, cells were active pharmaceutical and chemotherapeutic agents, and a fixed and permeabilized, and nuclei were stained and counted small number of natural products. Serial rounds of phenotypic at 48 hours (Operetta High-Content Imaging System; fi HTS identi ed ID-8 (1-[4-Methoxyphenyl]-2-methyl-3-nitro- PerkinElmer). 1 fi H-indol-6-ol), an inhibitor of the dual-speci city tyrosine- Raw images were automatically analyzed for nuclei segmen- 13 phosphorylation-regulated kinase 1A (DYRK1A) that induces tation, nuclei/cell counting, and cell area (Columbus 2.4.2 epithelial cell proliferation after injury in 2D and 3D culture Software; PerkinElmer). Proliferation rate or normalized cell systems. Wepropose that this compound may have the potential count (NCC) was calculated on the basis of nuclei counts at day to be developed into a therapeutic for AKI. 5normalizedto(1) live-cell count at day 3 (0 hour), (2) cell area at day 5, and (3) mean of eight free medium–treated control wells on each plate. Cells treated with library com- METHODS pounds or with the panel of controls were assigned as pro- liferating if NCC.1, nonproliferating if NCC=1, or dying if Cell Culture NCC,1. The assay robustness, reproducibility, and variability Primary HPTECs (Biopredic International, Saint-Grégoire, were evaluated by determining the Z-values across multiple fi France) from three different unique donors and NIH/3T3 - replicates using the panel of controls. broblasts (American Type Culture Collection no. CRL-1658) were used. Detailed methods are described in Supplemental Secondary Screen Material. Compounds with an average NCC.1.1 in the primary screen were taken forward to secondary screening. As in the primary Primary Screen screen, primary HPTECs were seeded in full medium. On day A primary screen of 1902 compounds was performed at the 1, full medium was replaced with free medium. On day 3, cells Institute of Chemistry and Cell Biology, Longwood Facility, were treated in triplicate with the selected compounds using a Harvard Medical School. Primary HPTECs were automatically D300 drug dispenser (Hewlett Packard) at 1, 3, 10, and 30 mM seeded in 96-well plates (WellMate; Thermo Scientific) in for 48 hours. After treatment, cells were counted as in the DMEM/Ham-F12 GlutaMAX medium (Thermo Scientific) primary screen. On day 5, 4 hours before fixing the cells, the supplemented with penicillin/streptomycin, hydrocortisone, modified thymidine analog EdU (Click-iT EdU Plus; Invitro- EGF, insulin-transferrin-selenium, and triiodothyronine gen) was added to mark proliferating cells. NCC was

J Am Soc Nephrol 29: 2820–2833, 2018 ID-8 Stimulates Tubular Proliferation 2821 BASIC RESEARCH www.jasn.org calculated as described in the primary screen section. We also Cell Proliferation in a 3D MPS Platform via evaluated the rate of proliferating cells on the basis of the Immunocytochemistry percentage of EdU-labeled cells in compound-treated wells The abilityofhitcompoundsto induceproliferation ofprimary compared with free medium controls to catch differences in HPTECs was tested in a 3D MPS. Cells were maintained for 48 proliferation based not only in the cell number. Detailed EdU hours in EGF-free medium (control) or damaged with 50 mM assay protocol is described in the Supplemental Material. of PMB. Subsequently, control cells were kept in EGF-free medium and PMB was substituted by EGF-free medium (un- treated) or treated for 48 hours with either 1 mM of ID-8 or In Vitro Damage Models harmine. Cell proliferation was assessed by staining for Ki-67 Induction of proliferation in primary HPTECs after damage and epcam, using immunocytochemistry.16 EdU-labeling was was assessed using four different in vitro models of acute cell not used to assess proliferation in the 3D MPS because of damage: (1)hypoxia(1%O, 29% of cell death), (2)15mM 2 extensive background signal from the matrix in the device. cadmium chloride (CdCl ; 16% of cell death), (3)5mM cyclo- 2 Antibodies are listed in Supplemental Table 1. sporin A (CsA; 12% of cell death), or (4)75mMpolymyxin (PMB; 11% of cell death) for 24 hours as described in the Kidney Injury Molecule-1 Expression Supplemental Material. In contrast to the screening phases, Effluents of kidney 3D MPS were analyzed for human kidney all supplements with the exception of growth factor EGF were injury molecule-1 (KIM-1) using the Mesoscale Diagnostics added back into the cell medium (EGF-free medium). Dam- Human KIM-1 Kit (K141JHD-2). Effluents from controls de- aged cultures were treated with two concentrations of the hit vices were collected at 24, 48, 72, and 96 hours. Effluents from a compounds from the secondary screen using D300 drug dis- 3D MPS damaged with 50 mM of PMB were collected at 24 and penser (Hewlett Packard). Cells were treated for 24, 72, or 96 48 hours and subsequently collected at 24 and 48 hours after hours and the proliferation effect was measured by compari- been treated with 1 mMofharmine,1mM of ID-8, or EGF-free son of compound-treated cell counts with the untreated con- medium (untreated). trol. After treatment, cells were fixed and nuclei were stained and counted (Operetta High-Content Imaging). Compounds Target Engagement that promoted cell proliferation in at least two different dam- To test DYRK activation, we performed a cell-free, active site– age models were used to treat cells after damage in a ten-point dependent, competition binding assay commercially known as dose range (2.15-fold serial dilution) from 0.1 to 100 mMfor KINOMEscan (DiscoverX), which quantitatively measured 96 hours, spanning the primary screen concentration. the ability of a compound to compete with an immobilized, The compound that demonstrated strongest proliferative active-site directed ligand. We tested ID-8 and harmine in 11- potential using NCC was used to treat cells along with inactive point, three-fold serial dilution starting at 30 mMagainst and active DYRK inhibitors analogs. Cells damaged for 24 DYRK1A and DYRK2. The assay was performed by combining hours with hypoxia, CdCl (15 mM), CsA (5 mM), or PMB 2 three components: DNA-tagged kinase, immobilized ligand, (75 mM) were treated with 1 mM of the lead compound or its and ID-8 or harmine in different concentrations. The ability of active and inactive analogs for 48 hours. Proliferation was both compounds to compete with the immobilized ligand was assessed by the percentage of EdU-labeled cells as this method measured via quantitative PCR of the DNA tag.17 evaluate actively proliferating cells and not just cell number. The compounds that demonstrated strongest proliferative Small Interfering RNA Transfection effects were confirmed by a dose response from 0.1 to 1 mM Small interfering RNA(siRNA)transfectionswere done in 384- to identify proliferation that could be induced by concentra- well platesfollowingthe same experimental design described in tions lower than 1 mM. To test the specificity of the prolifer- the in vitro damage models section. Transfection complexes ation effect, the compounds were also tested in NIH/3T3 were prepared in Opti-MEM medium using Lipofectamine fibroblasts using the same experimental design. Proliferation RNAiMax (Thermo Scientific) and human DYRK1A siRNA was measured on the basis of the percentage of EdU-labeled (10 nM final concentration, #s4401, Silencer Select; Thermo cells compared with the untreated control (EGF-free medium Scientific), following the manufacturer’s protocol. After dam- for HPTECs and 1% bovine calf serum for fibroblasts) in age, cells were treated for 24 hours with either DYRK1A both analyses. siRNA, ID-8 (1 mM), DYRK1A siRNA+ID-8 (1 mM), or siRNA negative control (short hairpin RNA). Transfection ef- Cell Culture in a 3D MPS ficiency was measured by DYRK1A protein expression, and Human kidney tissues were obtained from surgical resection knockdown effects on proliferation were on the basis of the of renal cell carcinoma performed at the University of Wash- percentage of EdU-labeled cells across tested groups. ington Medical Center (Seattle, Washington). Primary HPTECs were isolated, seeded, and cultured as previously de- Library Preparation and RNA Sequencing scribed.12 Detailed protocols are described in the Supplemen- RNA samples (n=3 per group) were checked for quality (RIN tal Material. value .8.0) and quantity using Agilent 2200 Bioanalyzer

2822 Journal of the American Society of Nephrology J Am Soc Nephrol 29: 2820–2833, 2018 www.jasn.org BASIC RESEARCH instrument and nanodrop (Thermo Scientific), respectively. Z-factor .0.32 among the 22 tested plates (Supplemental Fig- Library preparation, quality control, and bioinformatics anal- ure 1, A–C). We chose NCC.1.1 as cut-off for proprolifera- ysis using bcbio-nextgen18,19 are fully described in the Sup- tive effects, which lead to the selection of 129 compounds plemental Material. The dataset is available with the National (Figure 1D, Supplemental Table 2) involved in the activation Center for Biotechnology Information’s Gene Expression of a variety of pathways (Supplemental Figure 1D). Omnibus database under accession number GSE113039 (reviewer token: utgzgyeiftozbgp). A Secondary Screen Reveals Eight Compounds that Promote HPTEC Proliferation Immunofluorescence To confirm the activity of the 129 hit compounds identified in the Immunofluorescence was used to validate upregulated genes primary screen with an NCC.1.1, HPTECs were rescreened found in the transcriptomics study at the protein level (pro- against all 129 hits over four concentrations (1, 3, 10, and 30 liferating cell nuclear antigen [PCNA], E2F transcription factor mM) because many of the compounds selected are more specific 1[E2F1], andcyclinsB1, E2, andD1) andto analyze the effect of at low concentrations and activate multiple secondary targets at ID-8 and harmine on the cell cycle. Detailed protocols and higher concentrations (Figure 1D). Proliferation was measured antibodies are described in the Supplemental Material. using the same experimental design as described in the primary screen (Figure 1A) using two different methods: cell number in- Western Blotting crement, using NCC; and by induction of cells actively cycling, Protein expression of DYRK1Awas confirmed in HPTECs and measured by EdU incorporation. The secondary screen identified NIH/3T3 fibroblasts treated with ID-8 and harmine after dam- eight compounds that produced NCC.1.1inatleasttwoofthe age, using Western blotting. Detailed protocol and antibodies four tested concentrations compared with cells maintained in free are described in the Supplemental Material. medium (NCC=1, coefficient of variation ,15%; Figure 1E) and that increased the number of actively proliferating cells from 6% Statistical Analyses (free medium) to 10.6% (CGS21680), 8% (GDC-0152), 16.9% Data are presented as mean6SEM. Statistical difference as (SB505124), 13.1% (ZM336372), 10.8% (fasudil), 13% (ini- calculated by t test. Multiple group comparison was conducted parib), 7.3% (PD151746), and 14.4% (ID-8) (Figure 1F). by two-way ANOVA followed by Dunnett multiple compari- sons post hoc test. P,0.05 was considered significant and rep- Confirmatory Screen Reveals Four Compounds that resented by * when compared with corresponding controls or Promote HPTEC Proliferation after Damage by # when compared with other groups. We next assayed the eight compounds selected in the secondary screen for the ability to promote cell proliferation after injury. To that end, cells cultured inEGF-free mediumwere damaged for 24 RESULTS hours by hypoxia (1% O2), CsA (5 mM), PMB (75mM), orCdCl2 (15 mM), followed by treatment with each of the eight com- Primary Screen Reveals 129 Compounds that Promote pounds at each of the two concentrations that produced the HPTEC Proliferation strongest proproliferative effect in the secondary screen (Figure We tested 1902 compounds from the Selleck library for the 1, E and F): 10 and 30 mM (CGS21680, SB505124, iniparib, and ability to increase proliferation of HPTECs at 11 mM. Cells ID-8), 1 and 3 mM (GDC-0152 and fasudil), 3 and 10 mM cultured in supplement-free medium (free) were treated with (ZM336372 and PD151746) (Supplemental Figure 2). Cells individual compounds or maintained in free medium (con- that received only EGF-free medium postdamage were used as trol). Cell counts were performed immediately after treatment controls. Cells were treated for 96 hours, fixed, and nuclei were (0 hour) in live cells and 48 hours post-treatment after fixing stained, counted, and compared with the control group (Colum- and staining of the nuclei (Figure 1A). Cell proliferation was bus Image Analysis Suite) (Figure 2A). also measured in a panel of control conditions, full medium Treatment with compounds CGS21680 (30 mM), (positive control), free medium (negative control), or 0.1 mM ZM336372 (3 mM), PD151746 (10 mM), and ID-8 (10 mM) digoxin medium (toxic control), and assayed for cell number promoted significant increases in cell number after 24 hours of at 0 and 48 hours as described above (Figure 1B). NCC was damage in at least two different damage models. Time course used as a surrogate to the proliferation rate. Proproliferative studies using ten-point dose range (2.15-fold serial dilution) compounds had an NCC.1, nonproliferative compounds confirmed the observed increase in proliferation after injury had an NCC of 1, and toxic compounds had an NCC,1. when compared with cells receiving full medium or no treat- On the basis of the NCC values, the panel of controls ment (EGF-free medium) (Figure 2B). In the confirmatory showed a clear separation of positive, negative, and toxic con- assay, only ID-8 produced an increase in cell number after trols (NCC=1.85, 1, and 0.58, respectively) (Figure 1C). Assay damage across all damage models (P,0.05; fold change reproducibility was shown by a coefficient of variation of 7.9, [FC]=1.48 after CsA, 1.29 after CdCl2, 1.29 after PMB, and 4.8, and 6.6, respectively, and by a correlation coefficient of 1.36 after hypoxia) and was therefore selected for further 0.86 among duplicates. Assay sensitivity was demonstrated by characterization in the next set of experiments.

J Am Soc Nephrol 29: 2820–2833, 2018 ID-8 Stimulates Tubular Proliferation 2823 BASIC RESEARCH www.jasn.org

A Day 0 Day 1 Day 3 Day 5 Change to Pin-transfer Live-cell count Seed HPTECs Fix and stain Fixed-cell count supplement- compound (Digital Phase in 96w plates Nuclei (Hoechst) free medium library (11uM) Contrast)

Growth Factors

B C Proliferation Proliferation 2.0 2.0

1.5 1.5

1.0 Toxicity 1.0 Toxicity 2 Negative Control R = 0.86 0.5 Toxic Control 0.5 Positive Control Library Compound Normalized Cell Count (Rep 2) 0.0 Normalized Cell Count (Rep 2) 0.0 0.0 0.5 1.0 1.5 2.0 0.0 0.5 1.0 1.5 2.0 Normalized Cell Count (Rep 1) Normalized Cell Count (Rep 1)

D E F Concentrations Average NCC 1.75 1.8 18 CGS 21680 1.6 16 ID-8 1.50 SB505124 1.4 14 1.25 ZM336372 1.2 12 Fasudil 1.00 1.0 10 Iniparib 0.8 8 PD151746 0.75

NCC (48h to 0h) 0.6 6 GDC-0152

129 compounds in 0.50 Supplement-free 0.4 EdU-positive cells (%) 4

Supplement-free medium medium 0.25 1 3.2 10 32 1 3.2 10 32 Full medium M M 1 3 10 30 M

Figure 1. Screening selects eight potential proproliferative compounds in primary HPTECs. (A) Schematic of the experimental design for the identification of compounds with proliferative potential in primary HPTECs. (B) Control scatter plot shows NCC of positive control (cells maintained in supplemented full medium shown by red squares), negative control (cells maintained in supplement-free medium shown by green circles), and toxic control (cells treated with 0.1 mM digoxin shown by purple circles). (C) Library scatter plot showing NCC of primary HPTECs maintained in supplement-free medium and treated for 48 hours with each of the 1902 compounds of the Selleck library at 11 mM. Blue circles represent library molecules. Blue boxed region indicates zone of increased proliferation. Pink boxed region indicates zone of decreased proliferation and/or cell death. Correlation coefficient of duplicates =0.86. (D) Heat map depicting the NCC of HPTECs main- tained in supplement-free medium followed by 48 hours of treatment with the 129 compounds selected in the primary screen, in four concentrations (1, 3, 10, and 30 mM). (E) Detailed dose response curve after 48 hours of treatment with the eight compounds that produced increase in the NCC. Dose response curves compared with cells maintained in supplement-free medium (control). (F) Increase in the percentage of EdU-positive cells after 48 hours of treatment with the eight compounds. Data are represented by mean6SEM of the FC over cells maintained in supplement-free medium (control). n=3 biologic replicates per group.

DYRK Inhibitors Induce Tubular Cell Proliferation after analogs of DYRK inhibitors (AZ191, harmine, ID-8, INDY, Damage TC-S 7004, and TG 003) at 1 mM and proliferation was as- ID-8, the top hit identified in the damage repair assay, is a sessed by the percentage of EdU-labeled cells. Treatment for 48 DYRK1A inhibitor.13 To evaluate the ability of ID-8 and other hours with harmine and ID-8 produced a significant increase DYRK inhibitors to promote proliferation after damage, in cell proliferation (P,0.05) compared with the untreated cells were treated with three inactive analogs of DYRK inhib- group (EGF-free medium) after hypoxia (FC=1.39 and 1.58, itors (harmaline, harmane, and norharmane) and six active respectively), CdCl2 (FC=1.7 and 1.69, respectively), CsA

2824 Journal of the American Society of Nephrology J Am Soc Nephrol 29: 2820–2833, 2018 www.jasn.org BASIC RESEARCH

A Day 0 Day 1 Day 3 Day 4 Day 9 Change to Damage Treatment Seed HPTECs Fix and stain Fixed-cell count EGF- hypoxia/ with hit in 96w plates Nuclei (Hoechst) free medium chemical/drug compounds

NH3 H3N PtP Cl ClC

Growth Factors

B

CsA (5M) CdCl2 (15M) Hypoxia 45 25 35 ) ) 3 ) 3 40 3 20 30 35 25 30 15 20 25 10 20 15 5 10 15 Cell Number (x10 Cell Number (x10 Cell Number (x10 10 0 5 0.25 1 4 16 64 0.25 141664 0.25 1 4 16 64 M M M

PMB (75M) 45 ) 3 40 ID-8 35 CGS21680 30 ZM336372 25 PD151746 20 15 No treatment post damage Cell Number (x10 10 (EGF-free medium) 0.25 1 4 16 64 M

Figure 2. Confirmatory screen reveals four compounds promoting proliferation of primary HPTECs after damage. (A) Schematic of the experimental design for the identification of compounds with proliferative potential in primary HPTECs after in vitro drug-/chemical- induced damage and hypoxia-induced damage. (B) A ten-point dose range (2.15-fold serial dilution) shows the change in cell number promoted by 96 hours of treatment with the four selected hit compounds in ten different concentrations (0.1–100 mM) after 24 hours of damage with 5 mMCsA,75mMPMB,15mM CdCl2,orhypoxia(1%O2). Data are represented as mean6SEM of the FC over the untreated group (EGF-free medium). n=3 per group, three biologic replicates.

(FC=2.3 and 2.39, respectively), and PMB (FC=1.96 and 2.41, respectively), CsA (FC=2.4 and 2.39, respectively), and PMB respectively) (Figure 3A). Harmane and norharmane also pro- (FC=2.08 and 2.32, respectively). No significant proliferation moted significant cell proliferation after damage with PMB effect was observed in concentrations ,1 mM (Figure 3B) and (P,0.05; FC=1.59 and 1.56, respectively) but this effect was it was selected as the concentration for the next experiments. only observed in the PMB group and was lower than the ob- The specificity of the proliferation effect of ID-8 and harmine served effects of ID-8 and harmine, so these compounds were was tested in NIH/3T3 fibroblasts after damage. Harmine not tested further. To investigate whether proliferation pro- (1 mM) increased the number of actively cycling cells (P,0.05) moted by ID-8 and harmine could be induced at concentra- compared with untreated cells (1% bovine calf serum me- tions lower than 1 mM, HPTECs were damaged as previously dium) after hypoxia (FC=1.6), CsA (FC=2.1), and PMB described and treated for 48 hours with ID-8 and harmine at (FC=1.9). ID-8 did not induce any proliferation in NIH/3T3 range of concentrations from 0.0001 to 1 mM. Treatment with fibroblasts, thereby suggesting ID-8 to have specificity in stim- 1 mM of harmine or ID-8 promoted significant cell prolifera- ulating proliferation of HPTECs (Supplemental Figure 3). tion (P,0.05) compared with the untreated group after hyp- Wenext analyzed the effect of harmine and ID-8 on cell cycle oxia (FC=1.58 and 2, respectively), CdCl2 (FC=1.56 and 1.66, using HPTECs. Regardless of the group cells were mostly in G1

J Am Soc Nephrol 29: 2820–2833, 2018 ID-8 Stimulates Tubular Proliferation 2825 BASIC RESEARCH www.jasn.org

A Inactive Active B Analogues Analogues 3 3.5 3.0 2 * 2.5 2.0 * * Hypoxia 1.5 * 1 1.0 0.5 0 0.0 1 M 1 0.1 0.01 0.001 0.0001

3 3.5 3.0 * * 2.5 2 * CdCl2 (15uM) Harmaline 2.0 1.5 * 1 Harmane 1.0 Norharmane 0.5 0 0.0 ID-8 AZ 191 Harmine 1 M 1 Harmine 0.1 0.01 Untreated post damage 0.001 ID-8 0.0001 (EGF-free medium) INDY 3 TC-S 7004 3.5 * * * TG 003 3.0 % EdU-positive cells 2 % EdU-positive cells 2.5 * CsA (5uM) Untreated post damage 2.0 (EGF-free medium) 1.5 1 (FC to untreated cells post damage) (FC to untreated cells post damage) 1.0 0.5 0 0.0 1 M 1 0.1 0.01 0.001 0.0001

3 3.5 * 3.0 * 2.5 2 * * PMB (75uM) * 2.0 * 1.5 1 1.0 0.5 0 0.0 1 M 1 0.1 0.01 0.001 0.0001 M

# CDHarmine ID-8 15 # * # 100 * * * * 10 * *

75 5 % of cells 50

25 % of cells in S phase 0 0

CsA PMB CsA PMB CsA PMB CdCl2 CdCl2 CdCl2 Hypoxia Hypoxia Hypoxia Other M G2 S G1 Untreated Harmine ID-8

Figure 3. DYRK inhibitors ID-8 and harmine promote proliferation of primary HPTECs after damage. (A) Proliferation effect promoted by 48 hours of treatment with 1 mM of inactive (harmaline, harmane, and norharmane) and active (AZ191, harmine, ID-8, INDY, TC-S

7004, and TG 003) DYRK inhibitors analogs after 24 hours of damage with hypoxia (1% O2), 15 mMofCdCl2,5mMofCsA,or75mMof PMB (n=2 per group, 3–5 biologic replicates). (B) Dose response curve after 48 hours of treatment with ID-8 and harmine in HPTECs after 24 hours of damage with hypoxia (1% O2), 15 mMCdCl2,5mMCsA,or75mM PMB (n=3 per group, three biologic replicates). EdU-positive cells were normalized to the total cell number per well; Data are presented as mean6SEM of the FC over the untreated group (EGF-free medium). (C) Quantification of cells in different cell cycle phases after damage followed by 24 hours of treatment with

2826 Journal of the American Society of Nephrology J Am Soc Nephrol 29: 2820–2833, 2018 www.jasn.org BASIC RESEARCH phase (75%–85%), followed by S (9%–11%), G2 (5%–10%), NIH/3T3 fibroblasts protein lysates in control conditions and and M phase (0.1%–0.2%; Figure 3C). Treatment with 1 mM after damage (Figure 4B). Treatment of HPTECs with ID-8 significantly increased (P,0.05) cells in S phase com- DYRK1A siRNA for 24 hours resulted in .90% knockdown pared with untreated cells (EGF-free medium) after hypoxia of DYRK1A (Figure 4C) and promoted increased proliferation (12.8% versus 7.6%, respectively), CdCl2 (11.7% versus 6.8%, (P,0.05) compared with the untreated group after CdCl2 respectively), CsA (9.5% versus 7.9%, respectively), and PMB (FC=2.6), CsA (FC=2.4), and hypoxia (FC=2.1) (Figure (11.5% versus 9%, respectively). The fraction of cells in S 4D). Cells treated with siRNA negative control (short hairpin phase in the ID-8 group was also superior compared with RNA [shRNA]) showed no increase in proliferation compared the harmine group, suggesting higher potency of ID-8 com- with the control. Combination of ID-8+DYRK1A siRNA led pared with harmine in stimulating proliferation (Figure 3D). to higher levels of proliferation (P,0.05) compared with the untreated group after hypoxia (FC=2.4), CdCl2 (FC=4.1), and ID-8 Enhances HPTEC Proliferation after Damage in a mildly after PMB (FC=1.53; Figure 4D), demonstrating a po- 3D Culture MPS tential additive/synergistic effect on proliferation after phar- We next examined whether the proproliferative effects of ID-8 macologic and genetic inhibition of DYRK1A. Because this and harmine observed in primary HPTECs in a 2D culture was observed only after hypoxia and CdCl2 damage, it is pos- system would be recapitulated in 3D MPS. Under normal con- sible that the mechanism to initiate proliferation after ditions, primary HPTECs cultured in MPSs show little or no DYRK1A inhibition depends on the distinct mechanism of expression of the kidney damage biomarker KIM-1, indicating initiation of damage. the absence of tissue damage. Exposure of HPTECs to PMB (50 DYRK1A has been shown to control cell cycle entry via mM) significantly increased KIM-1 protein expression after 24 cyclin D1 upregulation in neonatal foreskin fibroblasts.20 We and 48 hours (P,0.05; mean, 226.5 pg/ml versus 36.2 pg/ml therefore measured expression of cyclin D1 by immunofluo- and 228.5 pg/ml versus 47.8 pg/ml, respectively), and was not rescence in the cells receiving ID-8 and DYRK1A siRNA (Fig- reversed by 24 hours of PMB washout (untreated) or by treat- ure 4E) to further clarify the mechanism by which ID-8 could ment with 1 mM of either ID-8 or harmine (P,0.05; mean: be inducing proliferation. Cells treated with DYRK1A siRNA 143, 145, and 130 pg/ml, respectively) (Supplemental Figure for 24 hours showed mild increased cyclin D1 expression 4A). KIM-1 expression reverted to normal levels after 48 hours (P,0.05) compared with the untreated group after CdCl2 of PMB withdrawal, independently of treatment with DYRK (FC=1.2), CsA (FC=1.2), and hypoxia (FC=1.4). However, inhibitors. Proliferation after HPTEC treatment with 1 mMof in the groups treated with the combination of ID-8+DYRK1A ID-8 after PMB-induced damage was not statistically significant siRNA, we observed a significant increase in proliferation but did trend toward increased proliferation (Supplemental Fig- compared not only with the untreated control after CdCl2 ure 4B), as shown by a higher number of Ki-67–positive nuclei (FC=2.1), CsA (FC=1.4), PMB (FC=1.4), and hypoxia (P=0.07; FC=2.37) compared with the untreated group (EGF- (FC=1.9), but also compared with DYRK1A siRNA treatment free medium). Harmine treatment did not show the same trend alone after CdCl2 (FC=2.2), PMB (FC=1.4), and hypoxia (P=0.9; FC=1.09). This result corroborates our previous 2D ex- (FC=1.85), extending the role of cyclin D1 in HPTEC prolif- periments showing a stronger induction of cell proliferation by eration induced by DYRK1A. ID-8 as compared with harmine and to cells receiving no treat- ment after damage. ID-8 Modulates Cell Cycle Responses Upregulating More Proproliferative Genes Target Engagement and Genetic Manipulation Studies To investigate the mechanisms underlying stimulation of pro- Demonstrate Pharmacologic Activity of ID-8 via liferation by ID-8 and harmine after damage, we performed Binding to DYRK1A RNA sequencing in undamaged cells (control) and in cells Toconfirm target engagement of DYRK by ID-8 we used a cell- damaged by 24 hours of hypoxia followed by treatment with free, active-site dependent, competition binding assay (KINO- 1 mM of ID-8, harmine, EGF (full medium), or EGF-free me- MEscan; DiscoverX) and investigated binding of ID-8 and dium (untreated). Quality control data for the sequencing harmine to DYRK1A and DYRK2. We demonstrated that protocol is shown in Supplemental Figure 5, A and B. Principal ID-8 targets DYRK1A (Kd=120 nM) but not DYRK2 component analysis showed clear separation of the cells treated (Kd.30,000 nM). Harmine, on the other hand, targeted with ID-8 or harmine away from the untreated and full DYRK1A (Kd=5.1 nM) and also DYRK2 (Kd=310 nM; Figure medium groups, as well as a separation from the control group 4A). Expression of DYRK1A was confirmed in HPTECs and (Figure 5A). Hierarchical clustering showed concordance

ID-8 or harmine. (D) Increment of cells in S phase promoted by the treatment with 1 mM of ID-8 or harmine compared with the untreated group after four types of damage (n=12–24 per group, two biologic replicates). Data are presented as the percentage of the total cell count. *P,0.05 compared with the untreated group; #P,0.05 compared with the harmine group.

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A ID-8 Replicate ID= 1 ID-8 Replicate ID= 2 ID-8 Replicate ID= 1 ID-8 Replicate ID= 2 DYRK1A Kd (nM)= 98 DYRK1A Kd (nM)= 150 DYRK2 Kd (nM)= >30000 DYRK2 Kd (nM)= >30000

-6 1×10 1×10-6 2.5×10-6 2.5×10-6 -7 -7 8×10 8×10 2×10-6 2×10-6 -7 -7 6×10 6×10 -6 -6 -7 -7 1.5×10 1.5×10

Signal 4×10 4×10 -6 -6 -7 -7 1×10 1×10 2×10 2×10 0 0 5×10-7 5×10-7 0.01 1 100 10000 0.01 1 100 10000 0.01 1 100 10000 0.01 1 100 10000 Harmine Replicate ID= 1 Harmine Replicate ID= 2 Harmine Replicate ID= 1 Harmine Replicate ID= 2 DYRK1A Kd (nM)= 4.3 DYRK1A Kd (nM)= 6 DYRK2 Kd (nM)= 340 DYRK2 Kd (nM)= 280 1×10-6 1×10-6 2×10-6 2×10-6 -7 -7 8×10 8×10 1.5×10-6 1.5×10-6 -7 -7 6×10 6×10 -6 -6 -7 -7 1×10 1×10

Signal 4×10 4×10 -7 -7 2×10-7 2×10-7 5×10 5×10 0 0 0 0 0.01 1 100 10000 0.01 1 100 10000 0.01 1 100 10000 0.01 1 100 10000 nM nM nM nM

B C C Untreated ID-8 Harmine 24h 48h 24h 48h 24h 48h C Untreated DYRK1A siRNA HPTEC B-Actin DYRK1A HPTEC B-Actin DYRK1A NIH/3T3 B-Actin

D E ID-8 6 2.5 # DYRK1A siRNA * * ID-8 + DYRK1A siRNA * # shRNA * * * 4 2.0

* * * * # * * * 2 1.5 * * * * * %EdU-positive cells (FC to untreated post damage) (FC to untreated post damage)

0 Cyclin D1 expression - mean intensity 1.0 CdCl2 CsA PMB Hypoxia shRNA CdCl2 CsA PMB Hypoxia

Figure 4. Inhibition of DYRK1A by harmine and ID-8 leads to proliferation of primary HPTECs. (A) Matrix of binding constants (Kd)and curve images for ID-8 and harmine competition binding assay against DYRK1A and DYRK2. The amount of kinase measured by quantitative PCR (Signal; y-axis) is plotted against the corresponding compound concentration in nanomolar in log10 scale (x-axis). (B) Expression of DYRK1A in HPTECs and NIH/3T3 fibroblasts protein lysates in control cells, in damaged untreated cells (EGF-free in HPTECs and 1% bovine calf serum in fibroblasts), or treated with ID-8 or harmine for 24 and 48 hours. (C) Confirmation of DYRK1A knockdown by Western blot. (D) Proliferation induced by DYRK1A knockdown after damage with 15 mMCdCl2,5mM CsA, 75 mMPMB. and hypoxia (1% O2). (E) Upregulation of cyclin D1 after inhibition of DYRK1A by siRNA, ID-8, or DYRK1A siRNA+ID-8. Data are presented as mean6SEM of the FC over the untreated group (EGF-free medium). *P,0.05 compared with the untreated group; #P,0.05 compared with DYRK1A siRNA group (n=12–24 technical replicates per group, two biologic replicates). C, control cells. among the biologic replicates and a distinct pattern of differ- number of genes (n=764) was significantly modulated by ID- entially expressed genes in the groups treated with ID-8 or 8 compared with the harmine (n=486) and the full medium harmine and the untreated group (Figure 5B). A higher (n=19) groups, showing that ID-8 promoted higher

2828 Journal of the American Society of Nephrology J Am Soc Nephrol 29: 2820–2833, 2018 www.jasn.org BASIC RESEARCH

ABControl_rep1 10 ID-8_rep2 ID-8 Untreated Harmine Untreated Control_rep1 2 ID-8_rep1 5 ID-8_rep3 1 Harmine_rep3 Harmine_rep1 Control_rep1 Harmine_rep2 0 0 -1

-2 PC2: 12% variance -5 Untreated_rep1 Untreated_rep3 Full medium_rep1

Untreated_rep2 Rep 3 Rep 1 Rep 2 Rep 1 Rep 2 Rep 3 Rep 3 Rep 1 Rep 2 Rep 2 Rep 1 Rep 3 -10 Full medium_rep3 Full medium_rep2

–10 0 10 PC1: 15% variance Groups Full medium Control Harmine Untreated ID-8

C D Upregulated Transcripts cell division ID-8 x Untreated Control x Untreated ID-8 x Untreated nuclear division cell cycle phase transition mitotic nuclear division mitotic cell cycle phase transition 134 5 110 regulation of cell cycle process 4 regulation of mitotic cell cycle 1 128 regulation of cell migration microtubule cytoskeleton organization chromosome segregation 36 nuclear chromosome segregation positive regulation of cell cycle DNA replication Harmine x No treatment sister chromatid segregation 0.120.090.06 Downregulated Transcripts Gene Ratio Control x Untreated ID-8 x Untreated nuclear division Harmine x Untreated cell division mitotic nuclear division p.adjust 168 1 64 cell cycle phase transition 0 mitotic cell cycle phase transition 1e-08 0 21 regulation of cell cycle process regulation of mitotic cell cycle 5e-09 21 chromosome segregation nuclear chromosome segregation Count microtubule cytoskeleton organization 30 60 Harmine x Untreated DNA replication 40 70 sister chromatid segregation 50 80 positive regulation of cell cycle cell cycle G1/S phase transition 0.06 0.09 0.12 Gene Ratio

Figure 5. ID-8 (1 mM) modulates cell cycle response, upregulating proproliferative genes. (A) Principal component analysis shows distinct distribution of the cells treated for 48 hours with ID-8 and harmine in comparison with undamaged cells (control), no treatment after damage, or treated with EGF (full medium) after hypoxia-induced damage. (B) Hierarchical clustering of genes differentially expressed between cells treated for 48 hours with ID-8 or harmine and untreated cells. (C) Venn diagrams showing the number of differentially upregulated and downregulated genes in cells treated for 48 hours with ID-8, harmine, and untreated cells; FC.1.5. (D) Gene ontology of the top modulated pathways in cells treated for 48 hours with ID-8 or harmine compared with untreated cells. transcription modulation than the harmine treatment (Figure genes belonging to the prereplication complex (cell division 5C). Pathway analysis revealed that ID-8 treatment was more cycle 6 [CDC6], Origin recognition complex subunit 1 potent than harmine on upregulating proproliferative cell cycle [ORC1], and Minichromosome maintenance complex compo- genes, notably PCNA, E2F1, MYC, cyclins E2, A2, and B1, and nent 2–7 [MCM2–7]) as compared with the untreated group

J Am Soc Nephrol 29: 2820–2833, 2018 ID-8 Stimulates Tubular Proliferation 2829 2830 AI RESEARCH BASIC BC

Mean intensity A (FC to untreated post damage) ora fteAeia oit fNephrology of Society American the of Journal 1.0 1.2 1.4 1.6 1.6 1.0 1.2 1.4 UntreatedHarmine ID-8 UntreatedHarmine ID-8 dl s M yoi dl s M Hypoxia PMB CsA CdCl2 Hypoxia PMB CsA CdCl2 Hypoxia PMB CsA CdCl2 Hypoxia PMB CsA CdCl2 * Hoechst Hoechst * www.jasn.org * Cyclin B1 PCNA * * * * * * EdU EdU * * D8Harmine ID-8 1.0 1.2 1.4 1.6 1.8 1.0 1.2 1.4 1.6 * * * Cyclin E2 * E2F1 Cyclin E2 E2F1 * * * * * Cyclin B1 PCNA MAP3K1 S-phase proteins CCNE2 E2F1 N DNAbiosynthesis DNA CCND1 PCNA RB1 DC ORC HDAC1 Merge Merge mScNephrol Soc Am J CCNA2 CDC6 CDC25B ID-8 CDK1 CCNB1 MCM2 PLK1 Log2FC 101 0 -1 29: PKMYT1 2820 SFN CDC45 – 83 2018 2833, www.jasn.org BASIC RESEARCH

(Figure 5D, Supplemental Figure 5C). On the other hand, the effects have been reported in trials with mesenchymal stem most upregulated genes in the untreated group compared with cells, concerns about maldifferentiation, tumorigenesis, and undamaged cells were related to immune response and inflam- overimmunodepression are still to be rigorously addressed.7 mation: leukocyte antigen complex (Major histocompatibility With the advent of large compound librariesand HTS meth- complex, class I, G [HLA-G] and B [HLA-B.5] and major his- ods, remarkable success was made in identifying potential tocompatibility complex, class II, DQ beta 1 [HLA-DQB1]) and therapeutic targets and lead candidate compounds stimulating the complement system (complement C1r [C1R] and 3 [C3]). proliferation of pancreatic b cells, hepatocytes, or podo- Upregulation of PCNA, E2F1, and cyclins B1 and E2 was con- cytes.9,10,14,24 In this study we took a similar approach and firmed at the protein level across different damage models (Fig- screened compounds under basal conditions for those that ure 6, A and B, Supplemental Table 3) after ID-8 treatment. As promoted increased cell proliferation. As a second step we observed in the transcriptomics data, ID-8 produced higher up- focused on investigating stimulation of repair after injury regulation of cell cycle genes at the protein level compared with and assessed the compounds with the strongest proprolifera- harmine, which did not induce upregulation of cyclin B1 and tive effects after different types of damage and validated the produced lower modulation of PCNA, E2F1, and cyclin E2. results in a 3D model. As a final step, we looked at the biologic Therefore, ID-8 promoted upregulation of genes involved in pathways targeted by the hit compounds. Among the four final cell cycle machinery showing the potential mechanism of pro- compounds that promoted proliferation of HPTECs after liferation after injury (Figure 6C). damage, the adenosine A2A receptor agonist CGS21680 was shown to preserve renal function, reversing fibrosis and re- ducing macrophage infiltration and inflammatory activation DISCUSSION in rat nephrotoxic nephritis.25 The remaining compounds ZM336372, a potent and selective c-Raf inhibitor, and Collectively, our early-stage discovery study identifies ID-8 as a PD151746, a selective, cell-permeable calpain inhibitor have potential therapeutic candidate to stimulate kidney tubular not been extensively studied in kidney regeneration and re- epithelial cell proliferation. By measuring proliferation of main interesting as potential new therapeutic agents. HPTECs in 2D and 3D in vitro models, we demonstrated The lead compound validated in our screen is a DYRK in- that inhibition of DYRK1A by ID-8 induces proliferation of hibitor that was recently described as targeting DYRK1A.13 HPTECs after multiple forms of tubular damage. Mechanis- Previously, DYRK2 and DYRK4 were described as the putative tically, the target engagement studies suggest the specificity of targets for ID-8,26 but a comprehensive evaluation of ID-8 ID-8 to bind to DYRK1A and transcriptomics experiments revealed its high specificity for DYRK1A and confirmed its identified key cell cycle regulators upregulated by ID-8 to me- lack of activity against DYRK2 and DYRK4.13 DYRKs are a diate cell proliferation. conserved family of eukaryotic kinases that are related to the Although HPTECs are known to promote tubular regener- cyclin-dependent kinases (Cdks), mitogen-activated protein ation after injury,21 the regenerative processes can be ineffi- kinases, glycogen synthase kinases, and Cdk-like kinases, play- cient, impaired, and dysregulated, resulting in extensive tissue ing key roles on cell proliferation and apoptosis induction.27 remodeling and fibrosis.22 One reason for inadequate repair Among its isoforms, DYRK1A and DYRK1B are negative may be that the mechanisms of tissue repair after AKI are regulators of the cell cycle promoting a switch to quiescent complex and involve epithelial, endothelial, stromal, and in- cellular state.28–30 Recently, DYRK1A inhibitors showed stim- flammatory cell types. This cellular complexity makes the task ulation of human pancreatic b cell replication, holding ther- of inducing repair through specific pathways difficult.7 De- apeutic promise for human diabetes.9,31 After testing different spite this complexity and heterogeneity, there are a number active and inactive DYRK inhibitors analogs, we identified of potential therapeutic approaches such as a-melanocyte– harmine, a DYRK1A inhibitor as well32 as a possible propro- stimulating hormone, recently licensed as ABT-719 for the liferative compound along with ID-8. However, harmine’sin- prevention of AKI in patients undergoing cardiac surgery; duction of cell proliferation was not corroborated by the 3D and QPI-1002, a siRNA targeting the p53 gene, currently in model and it had a smaller effect modulating gene and protein phase 1 clinical trials.23 Another promising approach uses expression compared with ID-8. Besides, harmine also in- mesenchymal stem cells and, although no serious adverse duced proliferation of NIH/3T3 fibroblasts showing less

Figure 6. ID-8 upregulates proproliferative proteins across different damage models. (A) Immunostaining images of all nuclei (Hoechst), actively cyclin cells (EdU), PCNA, E2F1, and cyclins B1 and E2. (B) Relative quantitation of PCNA, E2F1, and cyclins B1 and

E2 in HPTECs treated with 1 mM of harmine or ID-8 after 24 hours of damage with hypoxia (1% O2), 15 mMCdCl2,5mMCsA.or75mM PMB. *P,0.05 compared with the untreated group, (n=3 per group, two biologic replicates). Data are presented as mean6SEM of the FC over the untreated group (EGF-free medium). (C) Schematic representation depicting how ID-8 treatment after damage upregulates cell cycle genes, potentially leading to cell proliferation (generated by Integrated Network and Dynamical Reasoning Assembler: msb. embopress.org/content/13/11/954).

J Am Soc Nephrol 29: 2820–2833, 2018 ID-8 Stimulates Tubular Proliferation 2831 BASIC RESEARCH www.jasn.org specificity, thereby increasing the potential for off-target ad- V.S.V. and S.R. designed the study; M.B.M., S.R., V.C., and S.A.B. verse effects. carried out the two-dimensional experiments; E.J.W., K.A.L., and Recent studies have shown the role of cell cycle control in E.J.K. carried out the three-dimensional experiments; M.B.M. and AKI repair postdamage. After the first 24 hours of ischemic S.R. analyzed the data and prepared the figures; and M.B.M., S.R., injury, tubular cells undergo apoptotic and necrotic cell death. and V.S.V. wrote the manuscript. All authors approved the final In response, many of the surviving, normally quiescent prox- version of the manuscript. imal tubule epithelial cells proliferate and enter the cell cycle,33 Work in the Vaidya laboratory is supported by Outstanding New sequentially activating Cdks. This cell cycle reentry after injury Environmental Sciences award from NIH/National Institute of En- is viewed as a protective response. Transient expression of vironmental Health Sciences (NIEHS) (ES017543) and Innovation Cdk2 or Cdk4/6 inhibitors therefore represents a novel strat- in Regulatory Science Award from Burroughs Wellcome Fund egy to improve renal repair and could provide protection (BWF-1012518). M.B.M. was supported by the São Paulo Research against early tubular cell death and still allow for normal re- Foundation (grant 2016/04935-2). S.R. was supported by the Carl population of injured tubules via subsequent proliferation.7 In W. Gottschalk Research Scholar of the American Society of Ne- accordance with previous studies on DYRK inhibitors,9,31,34,35 phrology Foundation for Kidney Research. S.A.B. was supported by we observed that ID-8 upregulated genes involved in cell cycle the NIH P50 GM107618 and the Harvard Program in Therapeutic machinery like PCNA, E2F1, and cyclins E2 and B1 (Figure Science. E.J.K. is supported by NIH/National Center for Advancing 6C), showing the potential mechanism of proliferation after Translational Sciences (UH3TR000504 and UG3TR002158) and treatment. Cyclin D1 was not modulated in our transcriptom- NIH/NIEHS (P30ES007033). ics study; however, it has been described that knockdown of DYRK1A increase cyclin D1 at the protein level splitting cells into two fates, with one subpopulation accelerating the cell DISCLOSURES cycle and the other entering an arrested state.20 Our results S.R. is an employee of AstraZeneca and V.S.V. is an employee of Pfizer, Inc. showed increase in cyclin D1 expression after pharmacologic and genetic knockdown of DYRK1A, corroborating previous studies.20 REFERENCES The main caveat of our study is the absence of in vivo data to corroborate the in vitro efficacy findings. However, ID-8 in- 1. Li PK, Burdmann EA, Mehta RL; World Kidney Day Steering Committee 2013: Acute kidney injury: Global health alert. Kidney Int 83: 372–376, 2013 hibits the same family of kinases that induce proliferation in 2. 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J Am Soc Nephrol 29: 2820–2833, 2018 ID-8 Stimulates Tubular Proliferation 2833 ID-8 stimulates tubular proliferation SUPPLEMENTAL MATERIAL

Table of Contents Page 1 - Supplemental Methods 3 1.1 - Cell culture and reagents 3 1.2 - EdU proliferation assay 4 1.3 - Damage protocol 4 1.4 - Secondary screen (selection of the eight hit compounds- only HPTECs) 5 1.5 - In vitro damage models and selection of final compound - only HPTECs 5 1.6 - Experiment with different DYRK inhibitors after damage - only HPTECs 6 1.7 - Dose-response experiments with ID-8 and Harmine – HPTECs and 6 fibroblasts 1.8 - Cell isolation, culture and seeding in 3 dimensional microphysiological 6 system (3D MPS) platform 1.9 - Library preparation and RNAsequencing 7 1.10 Immunofluorescence 8 1.11 - Western blot 9 1.12 - References for Supplemental Methods 10 2 - Supplemental Tables 11 2.1 - Supplemental Table 1. List of antibodies used for immunocytochemistry, 11 immunofluorescence and western blot 2.2 - Supplemental Table 2. List of the selected 129 hit compounds in the primary 11 screen 2.3 - Supplemental Table 3. Fold change and p values of cell cycle proteins 15 modulated by the treatment with ID-8 or Harmine after different types of damage 3 - Supplemental Figures 16 3.1 - Supplemental Figure 1. Primary screen shows compounds with potential pro- 16 proliferative effects in primary human proximal tubular epithelial cells (HPTECs) 3.2 - Supplemental Figure 2. Compounds CGS21680, ID-8, ZM336372 and 17 PD151746 promoted proliferation of primary human proximal tubular epithelial cells (HPTECs) in, at least, two types of damage 3.3 - Supplemental Figure 3. DYRK1A inhibitor ID-8 does not promote 18 proliferation of NIH/3T3 fibroblasts after damage

Supplemental material 1

ID-8 stimulates tubular proliferation 3.4 - Supplemental Figure 4. ID-8 promotes proliferation of primary human 19 proximal tubular epithelial cells (HPTECs) in 3 dimensional microphysiological system (3D MPS) 3.5 - Supplemental Figure 5. RNA sequencing identifies differentially expressed 21 genes after ID-8 and Harmine treatment post-damage

Supplemental material 2

ID-8 stimulates tubular proliferation 1 - Supplemental Methods

1.1 - Cell culture and reagents

HPTECs were purchased from Biopredic International (Rennes, France). Cells were cultured in collagen VI-coated flasks with DMEM/Ham’s-F12 GlutaMAX medium

(ThermoScientific) supplemented with 100 IU/mL penicillin/100 μg/mL streptomycin

(Gibco), 36ng/mL hydrocortisone (HC, Sigma), 10 ng/mL epidermal growth factor (EGF,

Promega), 1% insulin-transferrin-selenium (ITS, Lonza), and 4 pg/mL triiodothyronine

(T3, Sigma) (Full medium). In screening experiments, HPTECs were kept in

DMEM/Ham’s-F12 GlutaMAX medium only supplemented with penicillin/ streptomycin

(Free medium). Cells were maintained at 37°C in a humidified 5% CO2 incubator and the medium was replaced one day after seeding and then every other day. For all experiments cells were used at passage 3.

Proliferation effect was compared to NIH 3T3 fibroblasts (ATCC, CRL-1658). Cells were cultivated in DMEM (ThermoScientific) supplemented with 10% bovine calf serum (BCS) and 100 IU/mL penicillin/100 μg/mL streptomycin (Gibco). In screening experiments BCS was reduced to 1%.

For the experiments with fibroblasts we followed the same experimental design used with HPTECs: cells were seeded in 96 well plates and kept in 1% bovine calf serum

(BCS) for 48 hours. Induction of damage was performed using three different in vitro models of acute cell damage. 1) Hypoxia: (1% O2); 2) 15µM, 10µM, 5µM and 2.5µM cadmium chloride (CdCl2); 3) 5µM cyclosporine A (CycloA) or 75µM polymyxin (PMB) for

24h. The 15µM of CdCl2 used to damage HPTECs induced complete cell death in fibroblasts and the experiments were carried out in three different concentrations (10µM,

5µM and 2.5µM) and we selected 5uM based on the amount of cell death of 20%,

Supplemental material 3

ID-8 stimulates tubular proliferation measured by cell number after damage compared to undamaged cells. After 24h of damage, cells were treated with ID-8 or Harmine from 0.1nM to 1uM for 48h, or kept in

1% BCS medium. The proliferation effect was measured based on the percentage of

EdU-labelled cells compared to the untreated control (1% BCS medium) in triplicates, from two biological replicates.

1.2 - EdU proliferation assay

To evaluate the percentage of actively proliferating cells four hours before fixing the cells, a modified thymidine analog, EdU (Click-iT EdU Plus, Invitrogen) was added to each well with a final concentration of 10uM. After the incubation period cells were taken out of the incubator and all procedures were carried out at room temperature: cells were fixed with 4% of paraformaldehyde for 20 minutes, permeabilized with 100% ice cold methanol for 10 minutes and washed 3 x with 3% BSA in 1x PBS. EdU incorporation and detection were performed according to manufacturer’s instructions. Nuclei were stained with 0.1 µg/ml Hoechst 33342 for 30 minutes in the dark. Fluorescence imaging was performed using an Operetta High-Content Imaging System (PerkinElmer) at 10X magnification, long WD objective, 17 fields/ well.

1.3 - Damage protocol

To test the ability of compounds to induce proliferation after damage, primary HPTECs in passage 3 were seeded in collagen VI-coated 96 well plates (10,000 cells/well) and

NIH/3T3 fibroblasts were seeded in 96 well plates (3,000 cells/well) using an automatic cell dispenser (WellMate, ThermoScientific). HPTECs were seeded in DMEM/Ham’s-F12

GlutaMAX medium (ThermoScientific) supplemented with 100 IU/mL penicillin/100

Supplemental material 4

ID-8 stimulates tubular proliferation μg/mL streptomycin (Gibco), 36 ng/mL hydrocortisone (HC, Sigma), 10 ng/mL epidermal growth factor (EGF, Promega), 1% insulin-transferrin-selenium (ITS, Lonza), and 4 pg/mL triiodothyronine (T3, Sigma) and fibroblasts in DMEM, 10% BCS and 100 IU/mL penicillin/100 μg/mL streptomycin (Gibco) (Full medium). On day 1 HPTEC full medium was replaced by new medium containing all the supplements described above, except for the EGF (EGF-free medium) and fibroblast full medium was replaced by DMEM, 10%

BCS. Because this experiment resulted in cell loss and cell damage supplement-free medium was replaced by EGF-free medium in order to prevent excessive cell death.

Cells were maintained in EGF-free medium or 1% BCS medium for 48 hours in order to abolish proliferation stimulus from the growth factor. On day 3 cells were either not damaged (control) or damaged with: 1) incubation at 1% O2 (Hypoxia); or 2) 15µM of cadmium chloride (CdCl2); or 3) 5µM of cyclosporine A (CycloA) or 75µM of polymyxin B

(PMB) in EGF-free medium for 24h. On day 4, cells were maintained in EGF-free or 1%

BCS medium (untreated and control groups) or treated with the following compounds:

1.4 - Secondary screen (selection of the eight hit compounds - only HPTECs): treatment with 10µM and 30µM of CGS21680; 1µM and 3µM of GDC-0152; 10µM and

30µM of SB505124; 3µM and 10µM of ZM336372; 1µM and 3µM of Fasudil; 10µM and

30µM of Iniparib; 3µM and 10µM of PD151746; or 10µM and 30µM of ID-8. Cells were treated for 24h, 72h and 96h.

1.5 - In vitro damage models and selection of final compound - only HPTECs: treatment with 0.1µM, 0.21µM, 0.46µM, 1µM, 2.1µM, 4.6µM, 10µM, 21µM, 46µM and

100µM of CGS21680; ZM336372; PD151746; or ID-8. Cells were treated for 96h.

Supplemental material 5

ID-8 stimulates tubular proliferation

1.6 - Experiment with different DYRK inhibitors after damage - only HPTECs: treatment with 1uM of Harmaline; Harmane; Norharmane; AZ191; Harmine; ID-8; INDY;

TC-S 7004; and TG 003. Cells were treated for 48h.

1.7 - Dose-response experiments with ID-8 and Harmine - HPTECs and fibroblasts: treatment with 1µM, 0.1µM, 0.01µM, 0.001µM and 0.0001µM of ID-8 or Harmine. Cells were treated for 48h.

All compounds were dissolved in 100% DMSO in 10mM stock concentration and were added to the cells using D300 digital dispenser (Hewlett Packard). DMSO final concentration was normalized for all samples, except for control group which did not receive DMSO. Each experiment was performed using 3 biological replicates, in 3 technical replicates.

1.8 - Cell isolation, culture and seeding in 3 dimensional microphysiological system (3D MPS) platform

Healthy portions of the surgical specimen were dissected, stored at 4°C in Hanks balanced salt solution buffer containing penicillin-streptomycin, and processed for isolation of HPTECs within 24h. Confluent monolayer cultures of HPTECs with passage numbers 1 through 4 were suspended with 0.05% Trypsin-ethylenediamine tetraacetic acid, washed, counted, and resuspended at a concentration of 15 to 20 × 106 cells/mL.

Approximately 5 μl of cell suspension were injected into the collagen IV–coated lumen of the 3D MPS platform (Nortis Inc.). Cells were allowed to adhere for 24 hours before

Supplemental material 6

ID-8 stimulates tubular proliferation initiating media flow at 0.5 μl/min. Cell coverage and integrity of the tubule structure were assessed under light microscopy on a weekly basis.

1.9 - Library preparation and RNA sequencing

RNA samples were isolated using RNeasy plus (Qiagen) (n=3 /group) and were checked for quality (RIN value>8.0) and quantity using Agilent 2200 Bioanalyzer instrument and nanodrop (Thermo Scientific), respectively. RNA-seq libraries were prepared using

Illumina TruSeq Stranded mRNA sample preparation kits (San Diego, CA) from 500ng of purified total RNA according to the manufacturer’s protocol. The finished dsDNA libraries were quantified by Qubit fluorometer and the quality was assessed by Agilent

Bioanalyzer 2200. Uniquely indexed libraries were pooled in equimolar ratios, which was quantitated by qPCR and then sequenced on two Illumina HiSeq High-Output run with single-end 75bp reads by the Biopolymers Facility at Harvard Medical School. All samples were processed using an RNA-seq pipeline implemented in the bcbio-nextgen project (https://bcbio-nextgen.readthedocs.org/en/latest/).1 Raw reads were examined for quality issues using FastQC

(http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to ensure library and sequencing suitability.

Reads were aligned to UCSC build mm10 of the Mus musculus genome, augmented with transcript information from Ensembl release 90 using STAR.2 Alignments were checked for evenness of coverage, rRNA content, genomic context of alignments, complexity and other quality checks using a combination of FastQC, Qualimap,3 MultiQC

(https://github.com/ewels/MultiQC) and custom tools (Supplemental Figure 4A). Counts of reads aligning to known genes were generated by featureCounts.4 Transcripts Per

Supplemental material 7

ID-8 stimulates tubular proliferation Million (TPM) measurements per isoform were generated by quasi alignment using

Salmon.5 Data was loaded into R using bcbioRNASeq R package.6 Covariate analysis, sample clustering and gene expression visualization were done with DEGreport R package.7 Differential expression at the gene level was called with DESeq2,8 using counts per gene estimated from the Salmon quasi alignments by tximport.9 Lists of differentially expressed genes were examined for gene ontology (GO) and KEGG term enrichment with clusterProfiler.10 In addition, a cut-off-free gene set enrichment analysis

(GSEA) was performed using clusterProfiler and weighted fold change calculations from

DESeq2.

1.10 Immunofluorescence

In order to validate upregulated genes found in the transcriptomics study at the protein level cells after treatment were fixed in 4% paraformaldehyde for 20’ and permeabilized with 100% ice cold methanol for 10’. Cells were blocked with Odyssey buffer (Li-cor) for

1h at room temperature and incubated with conjugated antibodies and 0.1 µg/ml

Hoechst 33342 overnight at 4°C. After incubation cells were washed 2x with 1x PBS-T and 2X with 1x PBS.

To stablish cell cycle phase we used a modified IF protocol previously described 11.

Briefly, four hours before fixing cells were pulsed with 10 µM of EdU (cycling cells,

ThermoScientific) and with Live/Dead fixable far-red dead cell stain (LDR, 1:2000,

ThermoScientific). After four hours of incubation cells were fixed, permeabilized and stained with anti-phospho-Histone H3 (chromosome condensation during mitosis) conjugated with Alexa 488 (Cell Signaling) and with 0.1 µg/ml of Hoechst 33342 (all nuclei) overnight at 4°C. After incubation cells were washed 2x with 1x PBS-T and 2X

Supplemental material 8

ID-8 stimulates tubular proliferation with 1x PBS. Fluorescence imaging was performed using an Operetta High-Content

Imaging System (PerkinElmer) at 10X magnification. Raw images were automatically analyzed for nuclei segmentation, intensity, roundness, border isolation and background

(Columbus 2.4.2 Software, PerkinElmer). Twelve technical replicates were conducted on each biological replicate. Antibodies are listed in Supplemental Table 1.

1.11 - Western blot

Cells were harvested and lysed with M-PER Mammalian Protein Extraction Reagent

(ThermoScientific) + 1X Halt protease and phosphatase inhibitor cocktail

(ThermoScientific). Protein concentrations were determined using the BCA protein assay kit (Pierce, ThermoScientific), and equal amount of protein (20μg/sample, n=5-6/group) was loaded and run on a pre-casted 4-20% polyacrylamide gel (Bio-rad) and transferred to PVDF membranes (Bio-rad). Membranes were blocked with 5% milk in 1x TBS-T (Cell signaling) for 1h at room temperature and incubated with primary rabbit monoclonal anti-

DYRK1A (Cell Signaling) overnight at 4o.C followed by horseradish peroxidase (HRP) linked anti-rabbit secondary antibody (Cell Signaling). For protein normalization membranes were striped with Restore™ Western Blot Stripping Buffer

(ThermoScientific) for 5’ and incubated with mouse monoclonal IgG anti-b-actin HRP linked (Santa Cruz) for 2h at room temperature. Bands were detected using enhanced chemiluminescence and captured with Synergy H1 Plate Reader (BioTek). Blots were quantified with the help of Image Studio Lite 5.2 software (Li-cor).

Supplemental material 9

ID-8 stimulates tubular proliferation 1.12 - References for Supplemental Methods

1. bcbio - nextgen. https://bcbio-nextgen.readthedocs.io/en/latest/. 2. Dobin A, Davis CA, Schlesinger F, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15-21. 3. García-Alcalde F, Okonechnikov K, Carbonell J, et al. Qualimap: evaluating next- generation sequencing alignment data. Bioinformatics. 2012;28(20):2678-2679. 4. Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014;30(7):923-930. 5. Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods. 2017;14(4):417- 419. 6. bcbioRNASeq: R package for bcbio RNA-seq analysis [computer program]. bcbioRNASeq: R package for bcbio RNA-seq analysis; 2017. 7. Report of DEG analysis [computer program]. Bioconductor version: Release (3.6); 2017. 8. Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550. 9. Soneson C, Love MI, Robinson MD. Differential analyses for RNA-seq: transcript- level estimates improve gene-level inferences. F1000Res. 2015;4:1521. 10. Yu G, Wang LG, Han Y, He QY. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012;16(5):284-287. 11. Hafner M, Niepel M, Subramanian K, Sorger PK. Designing Drug-Response Experiments and Quantifying their Results. Curr Protoc Chem Biol. 2017;9(2):96- 116.

Supplemental material 10

ID-8 stimulates tubular proliferation 2 - Supplemental Tables

Supplemental Table 1. List of antibodies used for immunocytochemistry, immunofluorescence and western blot

Protein Primary Dilution Secondary Dilution Ki-67 ab15580, Abcam 1:100 ab150080, Alexa 1:1000 Fluor, 594 Abcam Epcam ab20160, Abcam 1:100 ab150117, Alexa Fluor 1:1000 488, Abcam PCNA 8580, Alexa Fluor 488 conjugated, 1:500 - - Cell Signaling E2F1 AB208078, 1:500 - - Alexa Fluor 555 conjugated, Abcam CCNB1 SC-752, Alexa Fluor 488 conjugated, 1:500 - - Santa Cruz CCNE2 50-9714-80, Alexa Fluor 647 1:500 - - conjugated, eBioscience CCND1 MA1-39546, ThermoScientific 1:200 ab150117, Alexa Fluor 1:1000 488, Abcam Phospho- 3465S, Alexa Fluor 488 conjugated, 1:1000 - - Histone H3 Cell Signaling DYRK1A 2771, Cell Signaling 1:1000 7074 Anti-rabbit IgG, 1:10000 HRP linked, Cell Signaling B-actin SC-47778, (C4) HRP linked, Santa 1:10000 - - Cruz

Supplemental Table 2. List of the selected 129 hit compounds in the primary screen.

Std ID Compound Name Pathway Targets Replicate1 Replicate2 Average CV Dev 1 SB505124 TGF-beta/Smad TGF-beta/Smad 1.45 1.36 1.407 0.06 4.5% 2 GDC-0879 MAPK Raf 1.43 1.31 1.369 0.08 6.0% 3 GDC-0152 Apoptosis IAP 1.39 1.28 1.336 0.08 6.2% 4 BTZ043 Racemate Others Others 1.24 1.39 1.315 0.11 8.4% 5 N6022 Others Others 1.31 1.25 1.283 0.04 3.4% 6 SSR128129E Angiogenesis FGFR 1.26 1.29 1.274 0.02 1.4% 7 Birinapant Apoptosis IAP 1.31 1.23 1.269 0.06 4.6% Transmembrane 8 TAK-438 Potassium Channel 1.33 1.20 1.264 0.09 7.4% Transporters Fasudil (HA-1077) 9 Cell Cycle ROCK,Autophagy 1.30 1.20 1.252 0.07 5.3% HCl Neuronal 10 Phenacetin COX 1.22 1.25 1.233 0.02 1.4% Signaling Pritelivir (BAY 57- 11 Others Others 1.21 1.24 1.222 0.02 1.6% 1293) 12 SC-514 NF-κB IκB/IKK 1.21 1.22 1.218 0.01 0.4% 13 ZM 336372 MAPK Raf 1.22 1.20 1.209 0.01 1.0% Neuronal 14 Asaraldehyde COX 1.14 1.62 1.379 0.34 24.6% Signaling Transmembrane 15 Tolbutamide Potassium Channel 1.15 1.57 1.360 0.30 22.2% Transporters 16 SB525334 TGF-beta/Smad TGF-beta/Smad 1.33 1.33 1.332 0.00 0.0% Supplemental material 11

ID-8 stimulates tubular proliferation

Std ID Compound Name Pathway Targets Replicate1 Replicate2 Average CV Dev Rizatriptan Neuronal 17 5-HT Receptor 1.18 1.45 1.317 0.19 14.6% Benzoate Signaling Pancuronium Neuronal 18 AChR 1.53 1.07 1.299 0.32 24.7% dibromide Signaling Protein Tyrosine 19 Imatinib (STI571) PDGFR 1.15 1.36 1.254 0.14 11.5% Kinase Santacruzamate A 20 DNA Damage HDAC 1.32 1.18 1.250 0.10 8.3% (CAY10683) 21 Ronidazole Others Others 1.32 1.17 1.244 0.11 8.5% 22 AGI-5198 Metabolism Dehydrogenase 1.29 1.19 1.239 0.07 5.5% 23 Iniparib (BSI-201) DNA Damage PARP 1.19 1.28 1.235 0.07 5.3% Neuronal Adrenergic 24 Scopine 1.06 1.40 1.230 0.25 20.0% Signaling Receptor 25 Tigecycline Others Others 1.23 1.23 1.229 0.00 0.0% 26 INCB024360 Metabolism IDO 1.29 1.16 1.227 0.09 7.7% 27 Glipizide Others Others 1.11 1.34 1.226 0.16 13.0% 28 Sulfanilamide Others Others 1.18 1.27 1.223 0.07 5.4% Transmembrane 29 Tariquidar P-gp 1.31 1.13 1.222 0.13 10.2% Transporters 30 Cefditoren Pivoxil Others Others 1.14 1.30 1.222 0.11 9.4% 31 Trelagliptin Proteases DPP-4 1.24 1.19 1.218 0.04 3.0% Reverse 32 Nevirapine Microbiology 1.25 1.18 1.214 0.05 4.5% Transcriptase 33 CRT0044876 DNA Damage APE 1.25 1.17 1.212 0.06 4.8% Neuronal 34 Naloxone HCl Opioid Receptor 1.11 1.31 1.208 0.14 11.6% Signaling 35 FPH1 (BRD-6125) Others Others 1.38 1.04 1.207 0.24 19.8% Valproic acid Neuronal Autophagy,HDAC 36 0.99 1.41 1.202 0.29 24.4% sodium salt Signaling ,GABA Receptor Transmembrane 37 Phenytoin sodium Sodium Channel 1.19 1.22 1.202 0.02 1.7% Transporters 38 Praziquantel Others Others 1.31 1.09 1.200 0.15 12.7% 39 Artemisinin Others Others 1.24 1.15 1.197 0.07 5.4% 40 Laquinimod Others Others 1.31 1.08 1.192 0.16 13.7% 41 E-64 Proteases Cathepsin K 1.20 1.18 1.191 0.02 1.4% Oxytetracycline 42 Others Others 1.21 1.17 1.189 0.03 2.7% (Terramycin) 43 Chlorothiazide Others Others 1.25 1.13 1.189 0.09 7.4% 44 CORM-3 Others Others 1.14 1.23 1.189 0.06 5.3% 45 Lincomycin HCl Others Others 1.17 1.20 1.189 0.02 1.8% Phenoxybenzamine GPCR & G Adrenergic 46 1.24 1.14 1.188 0.07 6.1% HCl Protein Receptor 47 ID-8 Others Others 1.19 1.18 1.187 0.00 0.3% Histone 48 MM-102 Epigenetics 1.10 1.27 1.185 0.12 9.7% Methyltransferas e 49 Metolazone Others Others 1.27 1.09 1.183 0.13 10.8% Endocrinology & Estrogen/progest 50 Pregnenolone 1.18 1.18 1.182 0.00 0.2% Hormones ogen Receptor 51 Apocynin Others Others 1.11 1.25 1.181 0.09 8.0% 52 Tebipenem Pivoxil Others Others 1.18 1.19 1.180 0.01 0.6% 53 HA14-1 Apoptosis Bcl-2 1.20 1.16 1.180 0.02 1.8% 54 Probucol Others Others 1.23 1.13 1.179 0.07 6.1% 55 Nalidixic acid Others Others 1.22 1.14 1.178 0.05 4.5% 56 Thiamet G Others Others 1.21 1.15 1.178 0.04 3.6% Caspofungin 57 Others Others 1.25 1.11 1.178 0.10 8.4% Acetate 58 Atglistatin Others ATGL 1.18 1.17 1.176 0.01 1.0% Supplemental material 12

ID-8 stimulates tubular proliferation

Std ID Compound Name Pathway Targets Replicate1 Replicate2 Average CV Dev 59 Chloramphenicol Others Others 1.20 1.16 1.176 0.03 2.4% （6-）ε- 60 Others Others 1.14 1.21 1.175 0.05 3.9% Aminocaproic acid Epinephrine GPCR & G Adrenergic 61 1.29 1.06 1.175 0.17 14.1% Bitartrate Protein Receptor Fluocinolone 62 Others Others 1.26 1.09 1.174 0.12 10.2% Acetonide Neuronal 63 Etomidate GABA Receptor 1.08 1.27 1.172 0.13 11.2% Signaling 64 PF-04620110 Metabolism Transferase 1.27 1.08 1.170 0.13 11.5% 65 Moroxydine HCl Others Others 1.17 1.16 1.170 0.01 0.6% 66 Meprednisone Others Others 1.15 1.19 1.170 0.03 2.4% 67 Mirtazapine Others Others 1.25 1.09 1.169 0.11 9.5% Sodium 68 Others Others 1.18 1.16 1.169 0.02 1.6% Nitroprusside NMDA (N-Methyl-D- Neuronal 69 GluR 1.22 1.11 1.169 0.08 6.5% aspartic acid) Signaling Neuronal 70 Nefiracetam GABA Receptor 1.18 1.15 1.168 0.02 1.7% Signaling 71 CGS 21680 HCl Angiogenesis 5-alpha Reductase 1.28 1.05 1.168 0.16 14.1% Histone 72 EPZ5676 Epigenetics 1.17 1.16 1.167 0.01 1.0% Methyltransferas e 73 FPH2 (BRD-9424) Others Others 1.28 1.05 1.166 0.16 13.7% 74 Aminophylline Metabolism PDE 1.10 1.23 1.164 0.09 8.0% GPCR & G Endothelin 75 Bosentan Hydrate 1.16 1.17 1.162 0.01 0.8% Protein Receptor 76 D-Pantothenic acid Others Others 1.07 1.25 1.162 0.13 11.2% Endocrinology & 77 Andarine Androgen Receptor 1.01 1.31 1.160 0.21 17.7% Hormones 78 Methylprednisolone Others Others 1.05 1.26 1.158 0.15 12.9% 79 Articaine HCl Others Others 1.14 1.18 1.157 0.03 2.2% Chlorpheniramine Neuronal Histamine 80 1.00 1.31 1.157 0.22 18.9% Maleate Signaling Receptor Bepotastine Neuronal Histamine 81 1.02 1.29 1.155 0.19 16.8% Besilate Signaling Receptor WY-14643 (Pirinixic 82 Metabolism PPAR 1.15 1.15 1.154 0.00 0.0% Acid) 83 Penicillin G Sodium Others Others 1.16 1.15 1.154 0.00 0.2% 84 Limonin Others Others 1.22 1.08 1.149 0.10 8.6% 85 PD 151746 Proteases Cysteine Protease 1.16 1.14 1.149 0.02 1.3% 86 IM-12 PI3K/Akt/mTOR GSK-3 1.21 1.09 1.149 0.08 7.0% 87 Methoxsalen Others Others 1.06 1.24 1.148 0.12 10.9% 88 Valganciclovir HCl Others Others 1.13 1.16 1.148 0.02 2.1% Neuronal Adrenergic 89 Naphazoline HCl 1.16 1.13 1.147 0.02 1.7% Signaling Receptor Neuronal Adrenergic 90 Acebutolol HCl 1.14 1.15 1.147 0.01 0.6% Signaling Receptor Cytoskeletal 91 CK-636 Arp2/3 1.26 1.02 1.141 0.17 14.8% Signaling 92 FH1(BRD-K4477) Others Others 1.20 1.08 1.140 0.08 7.4% Eprosartan 93 Others Others 1.22 1.06 1.139 0.12 10.3% Mesylate 94 Salicylanilide Others Others 1.14 1.14 1.139 0.00 0.0% 95 Isovaleramide Others Others 1.20 1.08 1.138 0.09 7.6% 96 Edoxaban Metabolism Factor Xa 1.12 1.15 1.138 0.02 1.7% 97 Glycyrrhizic Acid Others Others 1.18 1.10 1.138 0.05 4.8% 98 VGX-1027 Others Others 1.22 1.05 1.136 0.12 10.3% 99 BV-6 Apoptosis IAP 1.21 1.07 1.136 0.10 8.7% Supplemental material 13

ID-8 stimulates tubular proliferation

Std ID Compound Name Pathway Targets Replicate1 Replicate2 Average CV Dev 100 Mitotane Others Others 1.00 1.27 1.136 0.20 17.3% 101 TIC10 PI3K/Akt/mTOR Akt 1.23 1.04 1.135 0.13 11.3% Cytoskeletal 102 Mdivi-1 Dynamin 1.11 1.16 1.135 0.03 2.9% Signaling Semagacestat 103 Proteases Gamma- secretase 1.16 1.10 1.133 0.04 3.7% (LY450139) 104 Levofloxacin Others Others 1.14 1.11 1.129 0.02 1.9% 105 AEBSF HCl Proteases Serine Protease 1.24 1.02 1.129 0.16 14.1% 106 Droperidol Others Others 1.05 1.21 1.128 0.12 10.3% Endocrinology & 107 Exemestane Aromatase 1.14 1.12 1.128 0.02 1.5% Hormones 108 Isotretinoin Metabolism Hydroxylase 1.25 1.00 1.126 0.18 15.8% 109 Ornidazole Others Others 1.10 1.15 1.124 0.04 3.4% Neuronal Histamine 110 Betahistine 2HCl 1.23 1.02 1.123 0.14 12.8% Signaling Receptor 111 Troxipide Others Others 1.10 1.15 1.123 0.03 2.7% 112 Pifithrin-α (PFTα) Apoptosis p53,Autophagy 1.04 1.21 1.123 0.12 10.9% 113 Inosine Others Others 1.22 1.02 1.123 0.14 12.6% Histone 114 C646 Epigenetics 1.13 1.12 1.123 0.01 0.9% Acetyltransferase 115 Dimethyl Fumarate Others Others 1.10 1.15 1.122 0.03 2.9% 116 Apixaban Metabolism Factor Xa 1.14 1.10 1.122 0.03 2.4% 117 Amprolium HCl Others Others 1.13 1.11 1.120 0.02 1.7% 118 Erdosteine Others Others 1.12 1.12 1.118 0.00 0.3% Histone 119 EPZ004777 Epigenetics 1.04 1.20 1.117 0.11 10.1% Methyltransferas e 120 Prednisone Others Others 1.12 1.11 1.115 0.01 0.8% 121 Chloroprocaine HCl Others Others 1.10 1.13 1.115 0.02 1.7% Empagliflozin (BI GPCR & G 122 SGLT 1.12 1.10 1.113 0.01 1.3% 10773) Protein Neuronal Histamine 123 Lafutidine 1.13 1.10 1.112 0.02 2.1% Signaling Receptor 124 Dibenzothiophene Others Others 1.12 1.10 1.111 0.02 1.5% Reverse 125 Etravirine (TMC125) Microbiology 1.02 1.21 1.110 0.13 12.1% Transcriptase Neuronal 126 Risperidone 5-HT Receptor 1.22 1.00 1.109 0.16 14.5% Signaling Reverse 127 Emtricitabine Microbiology 1.20 1.02 1.107 0.13 11.7% Transcriptase 128 SB216763 PI3K/Akt/mTOR GSK-3 1.11 1.10 1.104 0.01 0.8% 129 Vitamin B12 Others Others 1.11 1.10 1.103 0.01 0.6%

Supplemental material 14

ID-8 stimulates tubular proliferation

Supplemental Table 3. Fold change and p values of cell cycle proteins modulated by the treatment with ID-8 or Harmine after different types of damage ID-8 (1µM) Harmine (1µM)

CdCl2 CycloA PMB Hypoxia CdCl2 CycloA PMB Hypoxia (15µM) (5µM) (75µM) (15µM) (5µM) (75µM) PCNA* 1.3/ 1.4/ 1.1/ 1.1/ 1.16/ 1.3/ 1.1/ 1.1/ 0.0001 0.0001 0.0001 0.0001 0.0001 0.0001 0.0001 0.03 E2F1* 1.2/ 1.3/ 1.1/ 1.2/ NS 1.2/ 1.1/ NS 0.0001 0.0001 0.0001 0.0003 0.0001 0.0001 CCNB1* NS 1.2/ 1.1/ 1.3/ NS NS NS NS 0.01 0.02 0.01 CCNE2* 1.4/ 1.5/ NS NS 1.3/ NS NS NS 0.004 0.005 0.02 *Fold Change to untreated group (EGF-free medium)/adjusted p values

Supplemental material 15

ID-8 stimulates tubular proliferation

3 - Supplemental Figures

Supplemental Figure 1. Primary screen shows compounds with potential pro- proliferative effects in primary human proximal tubular epithelial cells (HPTECs).

A-C) Primary screen quality control. D) Main pathways activated by the hit compounds.

Supplemental material 16

ID-8 stimulates tubular proliferation

Supplemental Figure 2. Compounds CGS21680, ZM336372, PD151746 and ID-8 promoted proliferation of primary human proximal tubular epithelial cells (HPTECs) in, at least, two types of damage. Selection of the compounds promoting cell proliferation after damage with A) 15µM of CdCl2; B) 5µM of cyclosporine A; C) hypoxia (1% O2) and 75µM of polymyxin B. Data are represented as mean ± SEM of the total cell number. n=3/group, 3 biological replicates

Supplemental material 17

ID-8 stimulates tubular proliferation

Supplemental Figure 3. DYRK1A inhibitor ID-8 does not promote proliferation of NIH/3T3 fibroblasts after damage. Dose response curve after 48h of treatment with ID-8 and Harmine in NIH/3T3 fibroblasts after 24h of damage with hypoxia (1% O2), 5µM of CdCl2, 5uM of cyclosporine A (CycloA), or 75µM of polymyxin B (PMB) (n= 3/group, 2 biological replicates). EdU-positive cells were normalized to the total cell number per well. Data are presented as mean ±

SEM of the fold change over the untreated group (1% bovine calf serum medium, BCS). *P<0.05 after correction for multiple comparisons.

Supplemental material 18

ID-8 stimulates tubular proliferation

Supplemental Figure 4. ID-8 promotes proliferation of primary human proximal tubular epithelial cells (HPTECs) in 3 dimensional microphysiological system (3D

MPS). (A) KIM-1 expression in effluents from devices: without damage (control) for 24h,

48h, 72h and 96h and damaged with 50µM of polymyxin B (PMB) for 24h and 48h

Supplemental material 19

ID-8 stimulates tubular proliferation followed by 24h and 48h of polymyxin B washout (no treatment) or treatment with 1µM of Harmine or ID-8; (B) Ki-67 (white arrows) and epcam staining (green) in 3D MPS maintained in EGF-free medium (control) or damaged with 50µM of polymyxin B (PMB) followed by 48h treatment with 1µM of Harmine or ID-8 or no treatment (EGF-free medium) (*P< 0.05 after multiple comparisons). n=3-6 biological replicates/group

Supplemental material 20

ID-8 stimulates tubular proliferation

Supplemental Figure 5. RNA sequencing identifies differentially expressed genes after ID-8 and Harmine treatment post-damage. A) RNAseq analysis quality control showing the number of detected genes, low intronic and

Supplemental material 21

ID-8 stimulates tubular proliferation high exonic mapping rates for the tested samples. B) Sample-sample correlation heat map showing intra-group variation.

C) Panther classification system of the most upregulated genes after treatment with 1uM of ID-8 or Harmine

Supplemental material 22

SIGNIFICANCE STATEMENT

One potential therapeutic strategy for treating AKI, apart from supportive care, dialysis, and trans- plantation, is stimulating the proliferation of proximal tubular epithelial cells. The authors de- scribe use of high-throughput screening to identify ID-8, an inhibitor of dual-specificity tyrosine- phosphorylation-regulated kinase 1A (DYRK1A), as a first-in-class compound that stimulates kidney tubular epithelial cell proliferation after different types of acute damage in two- and three-di- mensional in vitro models. They also provide in vitro evidence that ID-8 is able to bind DYRK1A in primary human proximal tubular epithelial cells and stimulate proliferation after injury by upre- gulating cell cycle mediators. This early-stage dis- covery study identifies ID-8 as a potential thera- peutic candidate to stimulate regeneration and repair of epithelial cells in the kidney after acute damage.