© 2018. Published by The Company of Biologists Ltd. Retromer associates with the cytoplasmic amino-terminus of Polycystin-2. Frances C. Tilley1, Matthew Gallon1, Chong Luo2, 3, Chris M. Danson1, Jing Zhou2, and Peter J. Cullen1. 1School of Biochemistry, Biomedical Sciences Building, University of Bristol, Bristol, UK. 2 Harvard Center for Polycystic Kidney Disease Research and Renal Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA. 3 Kidney Disease Center, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, People’s Republic of China. aCorrespondence: [email protected] (PJC) t p ri c s u n a m d e t p e c c A • e c n e ci S ell C f o al n r u o J JCS Advance Online Article. Posted on 3 May 2018 ABSTRACT Autosomal dominant polycystic kidney disease (ADPKD) is the most common monogenic human disease, with around 12.5 million people affected worldwide. ADPKD results from mutations in either PKD1 or PKD2, which encode the atypical G-protein coupled receptor polycystin-1 (PC1) and the transient receptor potential channel polycystin-2 (PC2) respectively. Although altered intracellular trafficking of PC1 and PC2 appear as an underlying feature of ADPKD, the mechanisms which govern vesicular transport of the polycystins through the biosynthetic and endosomal membrane networks remain to be fully elucidated. Here, we describe an interaction between PC2 and retromer, a master controller for the sorting of integral membrane proteins through the endo-lysosomal network. We show that association of PC2 with retromer occurs via a region in the PC2 cytoplasmic amino- terminal domain, independently of the retromer-binding Wiskott-Aldrich syndrome and scar homologue (WASH) complex. Based on observations that retromer preferentially interacts with a trafficking population of PC2, and that ciliary levels of PC1 are reduced upon mutation of key residues required for retromer-association in PC2, our data is consistent with the identification of PC2 as a retromer cargo protein. t p ri c s u n a m d e t p e c c A • e c n e ci S ell C f o al n r u o J INTRODUCTION Mutations in PKD2, which encodes the calcium-activated calcium channel polycystin-2 (PC2), underlie around 15% of autosomal dominant polycystic kidney disease (ADPKD) cases (Koulen et al., 2002; Rossetti et al., 2007; Zhou and Pollak, 2015). ADPKD affects between 1 in 500 and 1 in 4000 people worldwide, and is characterised by the formation of multiple bilateral renal cysts, which have devastating consequences on organ function (Torres et al., 2007). PC2 is predominantly localised to the endoplasmic reticulum (ER), but is also found in the primary cilia of renal tubule epithelia in association with polycystin-1 (PC1) (Koulen et al., 2002; Yoder et al., 2002; Nauli et al., 2003). Here, the polycystin complex functions to modulate a wide variety of intracellular signalling pathways, including the canonical and non-canonical Wnt signalling, cyclic adenosine monophosphate, G-protein coupled receptor (GPCR) and mammalian target of rapamycin pathways (Nauli et al., 2006; Zhou, 2009; Chapin and Caplan, 2010; Fedeles et al., 2014). The absence of either polycystin protein from the primary cilium is sufficient to promote kidney cystogenesis, and a number of PKD1 and PKD2 mutants that are defective in ciliary trafficking are reported to be pathogenic (Ma et al., 2013; Cai et t p ri c al., 2014; Su et al., 2015). Several studies have therefore addressed the question s u n a of how PC1 and PC2 traffic to the primary cilium from compartments of the m d e biosynthetic membrane trafficking network, with roles for PC1:PC2 complex pt e c c formation, cleavage of PC1 at a juxtamembrane GPCR autoproteolytic site, VxP A • e ciliary targeting motifs, an internal PLAT domain in PC1 and Rabep1/GGA1/Arl3, c n e ci BBSome and exocyst trafficking modules having all been implicated (Hanaoka et S ell C f o al n r u o J al., 2000; Geng et al., 2006; Kim et al., 2014; Fogelgren et al., 2011; Su et al., 2014; Su et al., 2015; Xu et al., 2016). Many of the trafficking proteins implicated both in ciliogenesis and the delivery of ciliary-resident proteins to this organelle were first experimentally associated with canonical vesicular trafficking pathways (Sung and Leroux, 2013). Exocyst, for example, was initially characterised as being required for the vesicular transport of cargo proteins from the Golgi apparatus to the plasma membrane in yeast (Novick et al., 1980; TerBush et al., 1996). Members of the Eps15 homology domain (EHD) protein family, which have roles in early stages of ciliogenesis, have long been known to function in membrane remodelling processes within the endosomal network (Naslavsky and Caplan, 2011; Lu et al., 2015; Bhattacharyya et al., 2016). Additionally, a recent study has demonstrated localisation of the endosomal protein serologically defined colon cancer antigen-3 (SDCCAG3) to the basal body of primary cilia, and implicated its activity in ciliary targeting of PC2 (Yu et al., 2016). The concept that components of the endosomal trafficking network have been co- opted by cells in order to sustain normal cilia function is supported by a recent t p ri c study, in which stable isotope labelling with amino acids in culture (SILAC)-based s u n a quantitative proteomics of the retromer complex revealed PC2 as a putative m d e interaction partner (McMillan et al., 2016). Comprising subunits VPS35, VPS29 and pt e c c either VPS26A or VPS26B, retromer is an evolutionary conserved heterotrimer A • e which functions at the endosome membrane to promote the retrieval of c n e ci transmembrane proteins, or ‘cargo’, away from a degradative fate in the lysosome S ell C (Seaman et al., 1998; Koumandou et al., 2011; Gallon and Cullen, 2015). The f o al n r u o J absence of retromer is thus correlated with increased lysosomal targeting of protein cargo, and is exemplified by the loss of the glucose transporter GLUT1 and the β2- adrenergic receptor (β2-AR) that occurs upon VPS35 knockdown (Temkin et al., 2011; Steinberg et al., 2013). Retromer was initially described as a cargo-selective complex, but it also serves an additional function as a molecular scaffold (Seaman et al., 1998; Nothwehr et al., 1999; Seaman, 2004; Harbour et al., 2010; Fjorback et al., 2012). That is, retromer recruits and co-ordinates the activity of a variety of proteins to regulate cargo selection, the formation of intermediate tubular and vesicular recycling carriers, Rab guanosine triphosphatase (GTPase) cycling and cytoskeletal dynamics (Harbour et al., 2010; Gallon and Cullen, 2015). In this study, we present work validating the putative interaction between PC2 and retromer, and identify a motif in the amino-terminal domain of PC2 required for retromer-association. We find that localisation of a PC2 amino-terminal peptide to VPS35-positive endosomes is perturbed upon mutation of this motif, although interaction between full length PC2 and retromer appears to depend on multi-valent interactions. Our data show that exogenous PC2 preferentially interacts with retromer either when the carboxy-terminal domain of PC2, containing both an ER- t p ri c retention signal and a PC1 binding site, is truncated, or when co-expressed with s u n a PC1, suggesting that retromer associates with a trafficking population of PC2. In m d e addition, we find that the PC1 ciliary trafficking defect associated with PKD2 pt e c c knockout in mouse kidney tubule epithelial cells is not rescued to the same extent A • e with reintroduction of PC2 bearing mutations in the motif required for association c n e ci with retromer compared to wild-type PC2. S ell C f o al n r u o J MATERIALS AND METHODS Antibodies. Primary antibodies used in this study were rabbit polyclonal VPS35 (Abcam, ab97545, IF: 1/200), rabbit monoclonal VPS35 (Abcam, ab157220, clone EPR11501(B), WB: 1/2000), rabbit polyclonal VPS26A (Abcam, ab137447, WB: 1/1000), rabbit polyclonal VPS26B (Proteintech, 15915-1-AP, WB 1/250), rabbit polyclonal VPS29 (Abcam, ab98929, WB 1/500), mouse monoclonal GFP (Roche, 11814460001, clone 7.1 and 13.1, WB: 1/2000), rabbit polyclonal GFP (used for YFP staining) (Abcam, ab290, IF: 1/20,000), mouse monoclonal SNX1 (BD Transduction, 611482, clone 51/SNX1, IF: 1/100), mouse monoclonal SNX27 (Abcam, ab77799, clone IC6, WB: 1/500), rabbit polyclonal strumpellin (Santa Cruz Biotechnology, Inc., 87442, WB: 1/500), mouse monoclonal tubulin (Sigma-Aldrich, T9026, clone DM1A, WB: 1/5000), rabbit polyclonal PC2 (Santa Cruz Biotechnology, Inc., sc-25749, WB: 1/250), mouse monoclonal acetylated tubulin (Sigma-Aldrich, T6793, clone 6-11B-1, IF: 1/100,000), mouse monoclonal mCherry (Abcam, ab125096, clone IC51, WB: 1/2000), rabbit monoclonal GLUT1 (abcam, ab115730, IF: 1/500), mouse monoclonal LAMP1 (Developmental Studies t p ri c Hybridoma Bank, 1DB4, IF: 1/500), rabbit polyclonal DENND4C (Sigma-Aldrich, s u n a HPA014917, WB: 1/250), mouse monoclonal myc (AbD Serotec, MCA2200, clone m d e 7E12, WB: 1/2000), mouse monoclonal GST (Santa Cruz, sc-138, clone B-14, WB: pt e c c 1/1000), mouse monoclonal His (Sigma-Aldrich, H1029, clone HIS-1, IF: 1/1000), A • e and rabbit polyclonal FAM21 (a gift from D.D. Billadeau, Mayo Clinic, Rochester, c n e ci MN, WB: 1/1000). S ell C f o al n r u o J Plasmids. Amino-terminal (PC2-(1-48), PC2-(1-60), PC2-(1-70), PC2-(1-84), PC2- (1-94), PC2-(1-156) and PC2-(1-223)) and carboxy-terminal (PC2-(680-968)) fragments of PC2 were subcloned into either pEGFP-N1 or pEGFP-C1 from an original full-length PC2-containing plasmid, which was a gift from S. Somlo (Yale Nephrology, New Haven, CT). Primers for these reactions are listed in Supplementary Table 1 (ST1). Site-directed mutagenesis was used to introduce the point mutations p.R6G, p.V7A, p.P9A, p.E48A, p.Q49A, p.R50A, p.G51A, p.L52A, p.E53A, p.I54A, p.E55A, p.M56A, p.Q57A, p.R58A, p.I59A and p.R60A into PC2 (1-223-GFP), and the p.I54A and p.I59A mutations into full length PC2 and PC2- myc, using the primers listed in Supplementary Table 2 (ST2). PC2 (1-703-GFP) was cloned from HeLa cDNA into a pEGFP-N1 vector using the primers also indicated in ST1. Mouse PC2-GFP was generated, and the p.R7AxP9A mutation introduced, as previously described (Su et al., 2015). FAM21(1-356) was subcloned into pEGFPC1 from an original full length FAM21-containing plasmid, which was a gift from D.D. Billadeau (Mayo Clinic, Rochester, MN), and is initially described in Steinberg et al., 2013. YFP-PC1 was generated by inserting YFP t p ri c immediately downstream of the PC1 signal peptide as previously described (Su et s u n a al., 2014). mCherry-PC1 was a gift from P. Harris (Mayo Clinic, Rochester, MN). m d e mCherry-SNX1 was cloned as described in Hunt et al., 2013. pt e c c A • e c n e ci S ell C f o al n r u o J Production of lentivirally transduced RPE-1 cells. Previously described in McMillan et al., 2016. Production of PKD2 knockout kidney tubule cells. These cells were generated by isolating kidney tubule cells from the PKD2 knockout mouse using the marker DBA, followed by immortalisation with a temperature sensitive SV40 construct. Cell culture and DNA transfection. HEK293T (from ATCC, cat. # CRL-3216), hTERT RPE-1 (from ATCC, CRL-4000) and HeLa (from ATCC, cat # CCL-2) cells were cultured in DMEM (Sigma, D5796), supplemented with 10% (vol/vol) foetal bovine serum (FBS) (HEK293T and RPE-1: Sigma, F7524, HeLa: Gibco, 10270098) at 37°C, 5% CO . PKD2 knockout kidney tubule cells were routinely 2 cultured at 33°C, 5% CO in DMEM/F12 (50:50) (Corning cell grow, 10-090-CV) 2 supplemented with 10% FBS (Gibco, 10437-028) and 5U/ml interferon-gamma (Sigma, I4777) HeLa cells were transiently transfected with PC2 peptide constructs at 50-70% confluence using FuGENE-HD (Promega, E2311) and Opti-MEM (Gibco, t p ri c 31985062) according to the manufacturer’s instructions. HEK293T cells were s u n a transiently transfected at 80-90% confluence with various constructs using 25 kDa m d e linear PEI (polyethylenimine, Polysciences, 23966-2) and Opti-MEM. Cells were pt e c c processed for biochemistry or imaging either 24 or 48 hours following transfection, A • e depending on the nature of the DNA transfected. For PC1 trafficking assays in c n e ci PKD2 knockout cells, cells were transiently transfected at 70-80% confluence with S ell C PC2 and PC1 constructs using PEI and MEM medium (Mediatech, MT10010CV). f o al n r u o J After 24 hours, cells were moved to a 37°C incubator and serum starved in DMEM/F12 2% FCS with interferon-gamma withdrawal for 36 hours before processing for imaging experiments. siRNA. For both FAM21C and SNX27 suppression, cells were transfected with a mixture of four ON-TARGETplus siRNA oligos (Dharmacon, GE Healthcare, LQ- 0296678-01 and L-017346-01). For VPS35 suppression, cells were transfected with a mixture of two ON-TARGETplus oligos (Dharmacon, GE Healthcare, J- 010894-07 and J-010894-08). Cells were typically treated twice with targeting siRNA in order to achieve adequate knockdown. In all knockdown experiments, cells treated with a non-targeting siRNA with the sequence (5’- gacaagaaccagaacgcca[dTdT]-3’) were also included as a negative control. siRNA transfections were carried out using DharmaFECT1 (GE Healthcare, T-2001) and Opti-MEM with GlutaMAX supplement (Gibco, 51985034). Cells were processed for biochemistry or imaging either 72 or 96 hours following the first siRNA transfection. In order to assess levels of protein knockdown, cells were lysed in an appropriate volume of PBS-based lysis buffer (PBS pH7.4, 5mM EDTA, 1% Triton X-100 and complete protease inhibitor cocktail) and protein concentration t p ri c determined using BCA assay. Protein extracts were then analysed by standard s u n a Western blotting procedures. m d e pt e c c Immunofluorescence. A • e For fluorescence microscopy, cells which had been plated onto glass coverslips c n e ci were first fixed in 4% (vol/vol) paraformaldehyde in phosphate buffered saline (PBS) S ell C for 20 minutes before being washed 3x in PBS. The second wash was f o al n r u o J supplemented with 30mM glycine. Cells were then permeablised for 5 minutes in PBS 0.1% (vol/vol) Triton X-100, washed a further 3x in PBS and then blocked in PBS 1% (wt/vol) bovine serum albumin (BSA) for 1 hour at room temperature. Cells were then incubated in primary antibodies diluted in PBS 1% (wt/vol) BSA, also for 1 hour at room temperature. After a further 3x PBS washes, cells were incubated in fluorescently-conjugated secondary antibodies (Molecular Probes) diluted 1/400 in PBS 1% (wt/vol) BSA for 1 hour at room temperature. After a final 2x washes in PBS and 1x wash in distilled water, coverslips were mounted onto microscope slides using Fluoromount-G (eBioscience, 00–4958-02). If one of the proteins to be stained was the lysosomal associated membrane protein-1 (LAMP-1), then cells were permeablised in PBS 0.1% (wt/vol) saponin (Sigma-Aldrich, 47036), and all subsequent washing and staining steps were carried out in the presence of 0.01% (wt/vol) saponin. Live cell imaging. For live cell imaging, cells expressing fluorescently-tagged proteins were plated onto glass-bottomed MatTEK® dishes. Before imaging, growth media was removed and replaced with pre-warmed CO -independent media 2 (Gibco, 18045-054). Cells were then moved to a Leica SP8 AOBS confocal t p ri c microscope attached to a Leica DM I6000 inverted epifluorescence microscope, and s u n a imaged at 37°C for the required amount of time. m d e pt e c c GFP, mCherry and myc -immunoisolation and Western analysis. To A • e immunoprecipitate proteins labelled with either GFP, mCherry or myc tags, cells c n e ci expressing these constructs, either transiently or lentivirally, were lysed in a Tris- S ell C based immunoprecipitation buffer (20mM Tris, pH 7.4, 0.5% (vol/vol) Igepal plus f o al n r u o J