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The homophilic receptor PTPRK selectively dephosphorylates multiple junctional regulators to promote cell–cell adhesion

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Cite this article as: eLife 2019;8:e44597 doi: 10.7554/eLife.44597

Abstract

Cell-cell communication in multicellular organisms depends on the dynamic and reversible phosphorylation of protein tyrosine residues. The receptor-linked protein tyrosine phosphatases (RPTPs) receive cues from the extracellular environment and are well placed to influence cell signaling. However, the direct events downstream of these receptors have been challenging to resolve. We report here that the homophilic receptor PTPRK is stabilized at cell-cell contacts in epithelial cells. By combining interaction studies, quantitative tyrosine phosphoproteomics, proximity labeling and dephosphorylation assays we identify high confidence PTPRK substrates. PTPRK directly and selectively dephosphorylates at least five substrates, including Afadin, PARD3 and δ-catenin family members, which are all important cell-cell adhesion regulators. In line with this, loss of PTPRK phosphatase activity leads to disrupted cell junctions and increased invasive characteristics. Thus, identifying PTPRK substrates provides insight into its downstream signaling and a potential molecular explanation for its proposed tumor suppressor function.

https://doi.org/10.7554/eLife.44597.001

Introduction

Multicellular organisms have evolved elaborate mechanisms of intercellular communication in order to organize cells into functioning tissues. The phosphorylation of protein tyrosine residues is an essential feature of cell-cell communication and effectively coordinates diverse cell behaviors such as cell adhesion and motility in response to external stimuli. Kinases and phosphatases dynamically regulate phosphotyrosine levels, such that cells are primed to acutely respond to developmental cues or changes to their local environment. In particular, enzyme-linked cell surface receptors transduce external signals to the cell interior. For example, receptor tyrosine kinases (RTKs) dimerize upon ligand binding leading to trans-autophosphorylation, which recruits phosphotyrosine-binding proteins that propagate a variety of signaling cascades (Hunter, 2009). Protein tyrosine phosphatases (PTPs) are often thought to function in terminating or thresholding such signals (Agazie and Hayman, 2003). However, it is increasingly apparent that phosphatases themselves can propagate signals in response to growth factors; with the best example being PTPN11/SHP2; a key therapeutic target in cancer (Brown and Cooper, 1996). Moreover, many human PTPs are receptor-linked suggesting they can also receive input from the extracellular environment. The effects of protein phosphorylation are site-specific, for example, phosphorylation of Src Tyr419 upregulates kinase activity but phosphorylation of Tyr530 reduces it (Mohebiany et al., 2013). Thus, both kinases and phosphatases can modulate signaling cascades to affect cell behaviors. Despite this, the roles and substrates of the classical PTP family remain comparatively understudied.

The receptor type PTPs (RPTPs) are type one transmembrane proteins subdivided according to their extracellular domain (ECD) features. Like RTKs, RPTPs link extracellular sensing to intracellular catalysis. The regulatory mechanisms for most of the 21 RPTPs encoded by the human genome are poorly characterized (Tonks, 2006); however, it is known that the R2B RPTP subfamily form homophilic interactions and have been proposed to respond to cell-cell contact (Aricescu et al., 2007). There are four human R2B receptors: PTPRK, PTPRM, PTPRT and PTPRU, which share a common domain architecture of one MAM (meprin/A5/μ), one immunoglobulin (Ig)-like and four fibronectin (FN) domains combined with an uncharacterized juxtamembrane domain and tandem intracellular phosphatase domains; the first active (D1) and the second inactive (D2) (Figure 1A). Structural and biophysical studies suggest the PTPRM extracellular domain forms a rigid, pH-dependent, homophilic interaction in trans through the MAM-and Ig domains of one molecule and the FN1 and FN2 domains of another molecule, with the possibility of further cis interactions (Aricescu et al., 2007). Several cell adhesion proteins, such as cadherins and catenins, are proposed substrates for PTPRM (Craig and Brady-Kalnay, 2015). Its paralog PTPRK was identified as a candidate driver gene in mouse intestinal tumorigenesis by insertional mutagenesis (March et al., 2011; Starr et al., 2009) and was more recently identified as a gene fusion partner with the oncogene RSPO3 in a subset of human colorectal cancers (Seshagiri et al., 2012). Furthermore, single nucleotide polymorphisms (SNPs) within the PTPRK genic region are associated with inflammatory bowel diseases (IBDs) and type I diabetes age of onset (Inshaw et al., 2018; Trynka et al., 2011). PTPRK is regulated by a proteolytic cascade involving furin, ADAM10 and γ-secretase (Anders et al., 2006) and might function to dephosphorylate proteins such as EGFR (Xu et al., 2005) or STAT3 (Chen et al., 2015). PTPRK mRNA is broadly expressed, except in immune cells, skeletal muscle and testes (Figure 1—figure supplement 1A), and is upregulated by transforming growth factor β (TGFβ) signaling (Wang et al., 2005). Despite its importance in disease and signaling, the events downstream of PTPRK are not well established.

Figure 1 with 1 supplement see all
The homophilic receptor PTPRK is stabilized by cell-cell contact.

(A) Schematic of full length PTPRK. The extracellular MAM, Ig and fibronectin domains mediate homophilic interactions. The intracellular domain comprises a juxtamembrane domain and two PTP domains; one active (D1) and one inactive (D2). (B) Structured illumination microscopy images of MCF10As immunostained for PTPRK (F4 clone; magenta) and E-Cadherin (green). Graphs indicate fluorescence intensity through the Z-axis in indicated boxed regions. Scale bars = 10 µm. (C) Fluorescence microscopy images from co-cultures of wildtype and nuclear mApple-expressing PTPRK knockout MCF10As that were immunostained for PTPRK (magenta) and E-Cadherin (green). Nuclei were stained with Hoechst (blue). mApple positive PTPRK KO cells are indicated by orange asterisks. Cell junctions where PTPRK is absent are highlighted by white arrows. Scale bars = 20 µm. (D) MCF10As were plated at indicated densities and analyzed by immunoblot after 3 days in culture. Arrows indicate full length (top) and furin-cleaved PTPRK (bottom). See also Figure 1—figure supplement 1.

https://doi.org/10.7554/eLife.44597.002

Phosphatases present unique experimental challenges. For example, their signal, removal of phosphate, is inherently negative and means it is critical that they are studied in an appropriate context (Fahs et al., 2016). Given their homophilic interactions and subcellular localization, it is highly likely that the R2B family function at cell-cell contacts. We therefore reasoned that the appropriate context to assess their function would be in confluent, contact-inhibited epithelial monolayers. By combining proteomics approaches with in vitro and cell-based dephosphorylation assays we find that PTPRK displays striking substrate selectivity. In addition, there are distinct requirements for the two PTPRK intracellular phosphatase domains for substrate recognition. Multiple lines of evidence converge on five high confidence substrates: Afadin (AF6), PARD3 (Par3), p120Cat (p120-Catenin; CTNND1), PKP3 and PKP4 (p0071), which are known regulators of junctional organization. Indeed, PTPRK loss perturbs epithelial junction integrity and promotes invasive behaviors in spheroid cultures, consistent with its putative tumor suppressor role.

Results

PTPRK localizes to cell-cell contacts in epithelial cells

In order to detect endogenous PTPRK by immunoblot and immunofluorescence, we generated and characterized monoclonal antibodies against the purified PTPRK extracellular domain (ECD) (Figure 1—figure supplement 1B–D). Using one of our antibodies for structured illumination microscopy, we found PTPRK localized to puncta at basal cell-cell contacts that partially overlap with the adherens junction (AJ) protein E-Cadherin in MCF10A epithelial cells (Figure 1B). Homophilic interactions of the R2B receptor family have been demonstrated using suspension cell or bead aggregation assays (Brady-Kalnay et al., 1993; Gebbink et al., 1993; Sap et al., 1994; Zondag et al., 1995), and PTPRM-based structural and biophysical studies (Aricescu et al., 2006; Aricescu et al., 2007). To investigate homophilic PTPRK interactions in cells, we generated CRISPR/Cas9 PTPRK knockout (KO) MCF10A cells (Figure 1—figure supplement 1E), stably expressing nuclear mApple, and co-cultured them with unlabeled wildtype cells. By immunostaining, PTPRK is strikingly absent from cell-cell contacts between wildtype and adjacent KO cells, despite expression of other R2B receptors (Figure 1C and Figure 1—figure supplement 1F). Consistently, PTPRK protein levels increase with increasing cell density (Figure 1D). Finally, screening recombinant PTPRK ECD against a secreted protein microarray did not identify any additional ligands (Figure 1—figure supplement 1G). Thus, in combination, our data indicates homophilic trans-interactions stabilize PTPRK at cell-cell contacts in epithelial cells.

The PTPRK interactome reveals associations with cell adhesion regulators

To understand the function of PTPRK at cell-cell contacts we aimed to identify its direct substrates. Previous studies have described PTP substrate-trapping mutations, which correspond to D1057A and C1089S for the longest isoform of human PTPRK (Flint et al., 1997). We purified bacterially-expressed, biotinylated PTPRK wildtype and substrate-trapping intracellular domains (ICDs), as well as the pseudophosphatase D2 domain, and coupled them to streptavidin beads (Figure 2—figure supplement 1A and B) for affinity purification followed by mass spectrometry (AP-MS). We confirmed that the wildtype ICD could potently dephosphorylate tyrosine phosphorylated peptides, whereas the substrate traps and D2 domain were inactive, even at high concentrations (Figure 2—figure supplement 1C). To generate cell lysates enriched with tyrosine phosphorylated proteins, confluent MCF10A cells were treated with pervanadate, an irreversible PTP inhibitor (Figure 2A; Huyer et al., 1997). Excess vanadate was chelated with EDTA and endogenous PTP active site cysteine residues were alkylated with iodoacetamide, which was quenched by DTT, as previously described (Blanchetot et al., 2005). We confirmed that the substrate-trapping mutants bound tyrosine phosphorylated proteins (Figure 2—figure supplement 1D). Next, proteins bound to PTPRK domains after pull downs were trypsinized and identified by mass spectrometry.

Figure 2 with 3 supplements see all
The interactome of the homophilic adhesion receptor PTPRK.

(A) Experimental schematic of PTPRK interactome and substrate trapping studies. DA = D1057A, CS = C1089S. (B–D) Statistically enriched (p<0.05, n = 4) proteins after pull downs from pervanadate treated MCF10A lysates are displayed on volcano plots comparing PTPRK-ICD to beads control (B), PTPRK-ICD-DA to PTPRK-ICD (C) and PTPRK-ICD-CS to PTPRK-ICD (D). (E) GO term analysis of proteins statistically enriched (p<0.05) on PTPRK-ICD domains using Metascape. (F–G) Selected PTPRK interactors identified by mass spectrometry were validated by immunoblot analysis. Input and supernatants reveal the extent of protein depletion by recombinant proteins. Arrow indicates relevant band. See also Figure 2—figure supplements 1, 2 and 3. (H) Confluent, pervanadate-treated MCF10A lysates were used for pull downs with PTPRK D1057A ICD. Where indicated, pull downs were incubated with and without 20 mM vanadate for 30 min. 4% inputs (I), 4% supernatants (S), 4% eluates (E; following vanadate treatment) and pull downs (P) were subjected to immunoblot analysis. (I) Confluent, pervanadate-treated MCF10A lysates were treated with or without CIP to remove protein phosphorylation and were used for pull downs with PTPRK C1089S ICD. 4% inputs (I), 4% supernatants (S) and pull downs (P) were subjected to immunoblot analysis.

https://doi.org/10.7554/eLife.44597.004

Sixty-four proteins were >2 fold enriched (p<0.05; n = 4) on the wildtype PTPRK-ICD (Figure 2B and Figure 2—source data 1 and 2). We also screened for interactors using pervanadate-treated Hs27 Human fibroblast lysates (n = 3); another cell line that undergoes contact inhibition of proliferation (Figure 2—figure supplement 2A–C). We found that only 21% of the PTPRK-ICD interactome overlapped between MCF10A and Hs27 cells (Figure 2—figure supplement 2D), which might reflect differences in protein expression or phosphorylation between the cell lines. The first substrate trap (D1057A) enriched the serine/threonine kinase MAP4K4 and RAPGEF6, which were both recently linked to Hippo signaling (Figure 2C and Figure 2—figure supplement 2B; Meng et al., 2018). FMRP and the cell junction associated proteins PARD3, Afadin (AF-6/MLLT4) and PLEKHA6 were enriched on the second substrate trap (C1089S; Figure 2D and Figure 2—figure supplement 2C). Gene ontology (GO) term analysis for the PTPRK interactome highlights the enrichment of cell junction proteins across all domains (Figure 2E).

We used pull downs followed by immunoblotting to confirm interactions with previously reported PTPRK interactors (MINK1, PKP4, DLG5 and PTPN14 [St-Denis et al., 2016]) as well as proteins bound to the PTPRK substrate traps in this study, including FMRP-interacting NUFIP2. RAPGEF6, MAP4K4 and PARD3 were reproducibly enriched on substrate traps (Figure 2F and G). We did not observe interactions with previously reported R2B receptor substrates including E-Cadherin, β-Catenin, STAT3, EGFR (pY1068) and Paxillin (DEPOD database; Duan et al., 2015) besides p120Cat (Zondag et al., 2000), which was enriched on the C1089S trap along with PKP4 and NUFIP2 (Figure 2G). The principle of substrate trapping necessitates a direct interaction mediated by phosphotyrosine (Flint et al., 1997). We tested whether trapped proteins could be competed off PTPRK-D1057A using the phosphate mimetic orthovanadate. The MAP4K4 interaction with PTPRK D1057A ICD from pervanadate lysates was competed using orthovanadate, consistent with phosphotyrosine-mediated trapping (Figure 2H and Figure 2—figure supplement 2E). In contrast, Afadin was not depleted by orthovanadate treatment. Furthermore, PARD3, PKP4 and p120Cat bind the C1089S ICD less effectively in the absence of phosphorylation, also supporting the efficacy of the trapping approach (Figure 2I). However, we noted that all substrate-trapped proteins could still interact with PTPRK domains in phosphatase-treated lysates (Figure 2H and I) and most interactors can bind to the enzymatically active WT ICD (Figure 2F and G), indicating phosphorylation-independent PTPRK interactions. Furthermore, the PTPRK-D2 domain alone was sufficient to pull down approximately a third of PTPRK ICD interactors (Figure 2—figure supplement 3A and B; Figure 2—source data 2). Although substrate trapping was effective, our data indicate that because many proteins can bind PTPRK independently of phosphorylation or to its D2 pseudophosphatase domain (Figure 2F and G), trapping approaches alone could miss potential substrates.

To investigate interaction specificity further, we purified the ICD of the paralogous receptor PTPRM, which is 75% identical to PTPRK at the amino acid level (Figure 2—figure supplement 3C). Afadin, RAPGEF6 and NUFIP2 interact specifically with PTPRK, indicated by their biased depletion from supernatants. Interestingly, we found several that bound both PTPRK and PTPRM ICDs such as PARD3 and PKP4. Although MAP4K4, MINK1, PTPN14, DLG5 and p120Cat are depleted by both ICDs, they appear to have a higher affinity for PTPRK in pull downs (Figure 2—figure supplement 3D and E). Overall, the PTPRK interactome is enriched with cell junction-related proteins and shows partial overlap with PTPRM. Together, these data suggest that PTPRK and PTPRM have both unique and redundant roles at cell junctions.

The PTPRK dependent tyrosine phosphoproteome

Next, we reasoned that PTPRK deletion should result in the hyperphosphorylation of its substrates. To investigate this, we used quantitative tyrosine phosphoproteomics to compare wildtype and PTPRK KO MCF10A cells. We investigated the tyrosine phosphoproteome of confluent cells 24 hr post media change in order to observe residual phosphorylation, initially induced by EGF and/or serum growth factors. To this end, tyrosine phosphorylated peptides were enriched from trypsinized SILAC (stable isotopomeric versions of amino acids)-labeled wildtype and PTPRK KO MCF10A lysates using anti-pTyr Abs and biotin-tagged phosphotyrosine ‘superbinder’ mutant Src Homology 2 (SH2) domains (Tong et al., 2017) (Figure 3A and Figure 3—figure supplement 1A). We identified 282 quantifiable phosphotyrosine sites on 185 proteins (Figure 3—source data 1) from three experiments. Interestingly, 15 phosphosites were statistically upregulated in PTPRK KO cells compared to wildtype in at least two experiments, but only one site, in PAG1, was down regulated (Figure 3B). Strikingly, Afadin, PARD3 and PLEKHA6, which were all ‘substrate-trapped’ by PTPRK-C1089S, were amongst the proteins possessing enriched phosphosites in PTPRK KO cells (Figure 3B). Moreover, we identified upregulated phosphorylation in at least one experiment for p120Cat, PKP2, PKP3 and PKP4, which are δ-catenin family proteins and interact with the PTPRK ICD (Figure 3B and Figure 3—figure supplement 1B). Sites on KIAA1217 and Girdin were also upregulated in PTPRK KO cells, and analysis of our raw interaction data (Figure 2—source data 1) showed peptides for each protein were present in PTPRK pull downs, suggesting they are also potential substrates. Unfortunately, antibodies were not available to study them further. Critically, our total proteome analysis showed that the observed phosphosite levels on all proteins were not due to differences in protein amounts, except for PLEKHA6, which was not quantified (Figure 3C and Figure 3—source data 1 and 2). Beyond PTPRK-interacting proteins we found upregulated phosphosites on several other cell-cell adhesion regulators as well as ST5, ARHGAP5 and the receptor DCBLD2 (Figure 3B and D). Interestingly, DCBLD2 was previously identified as a PTPRK-interacting protein in a large-scale AP-MS study (Huttlin et al., 2017). In contrast, specific sites on Paxillin, EGFR and STAT3 were not changed or were undetectable (Figure 3B and Figure 3—source data 1). Thus, by combining the PTPRK interactome with tyrosine phosphoproteomics we have identified eight candidate substrates (Figure 3—figure supplement 1C).

Figure 3 with 2 supplements see all
The PTPRK dependent tyrosine phosphoproteome.

(A) Schematic of workflow to enrich and identify phosphotyrosine peptides from SILAC-labeled wildtype and PTPRK KO MCF10As. Equal amounts of wildtype and PTPRK KO cell lysates were combined prior to trypsinization. A 10% sample was reserved for total proteome analysis. Tyrosine phosphorylated peptides were enriched using anti-phosphotyrosine antibodies and SH2 domain ‘superbinders’. (B) Volcano plot of tyrosine phosphosites detected in PTPRK KO and wildtype MCF10As. Phosphosites > 50% enriched in (p<0.05; n = 3) in PTPRK KO cells are labeled red and those enriched in wildtype are blue. FDR = 0.01, two valid values required. (C) Volcano plot of protein abundance. Proteins > 50% more abundant (p<0.05; n = 3) in PTPRK KO MCF10As are shown in red, and wildtype in blue. FDR = 0.01, two valid values required. (D) Overview of proteins with at least one tyrosine phosphorylation site increased in PTPRK KO cells as determined by quantitative proteomics (FDR = 0.01, one valid value required). Tyrosine phosphosite change in PTPRK KO cells compared to wildtype is indicated by colored circles:>3 fold up; purple,>1.5 fold up; red,<1.5 fold up or down (no change); grey. Proteins identified as interactors by AP-MS or immunoblotting in this study are highlighted in bold and italics. *Denotes proteins enriched on substrate traps. See also Figure 3—figure supplements 1 and 2.

https://doi.org/10.7554/eLife.44597.010

Using these candidate substrates, we next aimed to determine any sequence selectivity by PTPRK. Previously, Barr et al. (2009) tested recombinant PTPs against a panel of phosphopeptides and observed limited sequence selectivity. For example, PTPRK showed reduced activity against peptides with basic residues in the three positions N-terminal to phosphotyrosine, including an EGFR-pY1068-containing peptide. In contrast, PTPRB showed no sequence preference (Barr et al., 2009). To investigate whether our candidate substrates shared common features we generated a consensus sequence, which showed a slight bias against basic residues immediately adjacent to the phosphotyrosine (Figure 3—figure supplement 1D). This is consistent with the positively charged PTPRK active site entrance observed in its crystal structure, which may preclude binding of positively charged or basic amino acids (Figure 3—figure supplement 1E). We next searched the phosphosite plus database with a seven amino acid consensus sequence phosphotyrosine and cross-referenced to the PTPRK interactome (Figure 2—source data 1). Beyond the candidate substrates, we identified an additional 18 phosphosites matching the consensus including substrate-trapped MAP4K4 and junction-associated ABLIM3 (Matsuda et al., 2010). In contrast, when we scrambled the consensus sequence we found fewer PTPRK interactors were identified (Figure 3—figure supplement 1F). Therefore, PTP substrate consensus sequences might be useful in expanding a candidate substrate list when interactors are known, but most likely only represents a permissive sequence for dephosphorylation, rather than a strict requirement.

Based on our data and these analyses, PKP3, MAP4K4 and ABLIM3 were also included as candidate substrates after confirming interactions with PTPRK and PTPRM domains (Figure 3—figure supplement 2A and B). A GO term analysis of statistically-enriched phosphosites from at least one sample (Figure 3D and Figure 3—figure supplement 2C) showed a bias towards proteins with roles in cell junction and actin cytoskeleton organization. Interestingly, several phosphosites identified here are growth factor- and, in most cases, Src kinase-dependent (Reddy et al., 2016). Importantly, however, the Src family kinase activating phosphotyrosine (e.g. Src-Y419) is 1.6-fold lower in PTPRK KO cells, therefore such kinase activity does not explain the observed differences (Figure 3—source data 1). Thus, PTPRK influences the tyrosine phosphorylation of numerous interacting proteins in cells, suggesting it has non-redundant cellular phosphatase activity.

PTPRK interacts with candidate substrates in confluent MCF10A cells

To investigate proximity interactions of proteins identified by AP-MS and phosphoproteomics in confluent cells we used BioID (Roux et al., 2012). We confirmed the cell surface localization of mutant BirA and flag-tagged PTPRK-C1089S and truncated PTPRK, lacking an ICD, by immunostaining. Truncated PTPRK showed notably stronger staining at the cell surface than PTPRK-C1089S, perhaps reflecting the loss of an endocytic or degradative signal in the ICD (Figure 4—figure supplement 1A). Immunoblots of pulldowns from doxycycline-induced, confluent cells revealed enrichment on PTPRK-C1089S over the truncated form for the candidate substrates Afadin, PARD3, p120Cat, PKP3, PKP4, as well as ABLIM3 and EGFR, but not E-Cadherin, Paxillin, β-Catenin, Tubulin or ZO2 (Figure 4A and B, and Figure 4—figure supplement 1B). Importantly, MINK1, PKP4, PTPN14 and DLG5 were also enriched and were previously identified by PTPRK BioID in HEK293 cells (St-Denis et al., 2016), lending additional support to our observations (Figure 4C). These data confirm that several of the interactors identified by AP-MS and phosphoproteomics experiments also interact with PTPRK in confluent MCF10A cells.

Figure 4 with 1 supplement see all
PTPRK interacts with candidate substrates in confluent MCF10A cells.

(A) Representative immunoblot analysis of biotin pull downs from MCF10As expressing tGFP or PTPRK BioID constructs. See Materials and methods for details. Red and blue arrows indicate exogenous and endogenous PTPRK, respectively. (B) Quantification of BioID immunoblots. Green bars indicate the number of times a protein was enriched on PTPRK-C1089S.BirA*-Flag, compared to PTPRK.ECD +TMD.BirA*-Flag in separate experiments. Purple bars indicate the number of times a protein was not enriched or was not detected in any pull downs. n ≥ 1. (C) Schematic representation of PTPRK proximity-labeling by BioID. PTPRK extracellular domain homology model is based on PTPRM (PDB: 2V5Y; Aricescu et al., 2007). Proteins within the dotted lines were detected in pull downs from indicated BioID lysates. Proteins not detectably biotinylated are listed on the left. Proteins in bold and italics were previously identified as PTPRK interactors using BioID in HEK293 cells (St-Denis et al., 2016). See also Figure 4—figure supplement 1.

https://doi.org/10.7554/eLife.44597.015

PTPRK directly and selectively dephosphorylates polarity and junctional proteins

We next sought to determine whether PTPRK could directly dephosphorylate any of its binding partners in vitro, with a particular focus on proteins that were hyperphosphorylated in PTPRK KO cells. Phosphatases have a reputation for promiscuity therefore we included the intracellular domain of the closely related receptor PTPRM and assayed a panel of negative controls. Using an in vitro para-nitrophenylphosphate (pNPP) colorimetric dephosphorylation assay, we determined that a three-fold higher molar ratio of PTPRM was required to match PTPRK activity (Figure 5—figure supplement 1A), consistent with a previous study (Barr et al., 2009). Interestingly, a three-fold higher molar ratio of PTPRK-ICD was required for equivalent activity to the D1 domain, suggesting the D2 reduces D1 enzyme activity (Figure 5—figure supplement 1A).

To identify proteins dephosphorylated by PTPRK, pervanadate-treated MCF10A cell lysates were incubated with recombinant protein domains, followed by phosphotyrosine immunoprecipitation and immunoblotting (Figure 5A). We expected dephosphorylated proteins to be depleted from immunoprecipitates but present in supernatants, or, as observed for PKP4, to show a shift in molecular weight. In these assays phosphoproteins from different reactions were equally enriched by IP, as indicated by phosphotyrosine immunoblots, but the lysates incubated with active phosphatase domains had fewer phosphoproteins overall based on depletion from supernatants (Lower panel; Figure 5B). Consistent with our interaction data, several previously reported R2B receptor substrates including E-Cadherin, STAT3, β-Catenin, Paxillin and EGFR-pY1068 (Duan et al., 2015), were not dephosphorylated by either PTPRK or PTPRM under these conditions (Figure 5B and Figure 5—figure supplement 1B-C). In contrast, the PTPRK ICD, but strikingly not the PTPRK-D1 or PTPRM domains, completely dephosphorylated Afadin (Figure 5B and Figure 5—figure supplement 1B), suggesting a combined role for the D1 and D2 domains in its recognition and selective dephosphorylation. PARD3 and PKP3 were preferentially dephosphorylated by the PTPRK and PTPRM ICDs. In contrast, the PTPRK and PTPRM D1 domains alone were sufficient to dephosphorylate ABLIM3, PKP4 and p120Cat (Figure 5B). Conversely, RAPGEF6 and MINK1 were not clearly dephosphorylated by the domains under these conditions (Figure 5—figure supplement 1B and C). MAP4K4, FMRP and NUFIP2 were not detectably tyrosine phosphorylated in the cell lysates, precluding us from assessing dephosphorylation (Figure 5—figure supplement 1C). It has been suggested for the R2A RPTPs that the inactive D2 domain can inhibit the D1 domain (Wallace et al., 1998). However, addition of PTPRK-D2 to PTPRK-D1 did not affect its activity against, for example, p120Cat (Figure 5B). In combination with our interaction studies, these data suggest that PTPRM and PTPRK have overlapping substrate specificities for δ-catenin proteins, ABLIM3 and PARD3, and the PTPRK-ICD selectively dephosphorylates Afadin.

Figure 5 with 2 supplements see all
PTPRK directly and selectively dephosphorylates cell junction regulators.

(A) Workflow of in-lysate dephosphorylation assay. Recombinant PTPRK and PTPRM domains were incubated with pervanadate-treated MCF10A lysates for 1.5 hr at 4°C, followed by immunoprecipitation of tyrosine phosphorylated proteins. (B) Pervanadate-treated MCF10A lysates were incubated with the indicated domains at an amount pre-determined to give equal phosphatase-activity prior to phosphotyrosine immunoprecipitation and immunoblot analysis. (C) Pull downs using chimeric RPTPs from confluent, pervanadate-treated MCF10A lysates were subjected to immunoblot analysis. (D) Pervanadate-treated MCF10A lysates were incubated with the indicated domains prior to phosphotyrosine immunoprecipitation and immunoblot analysis. See also Figure 5—figure supplements 1 and 2.

https://doi.org/10.7554/eLife.44597.017

To further investigate the role of the PTPRK and PTPRM domains in substrate selectivity, we generated chimeric proteins consisting of combinations of the PTPRK and PTPRM D1 and D2 domains (Figure 5C and Figure 5—figure supplement 1D). In pull down assays, we found that PARD3 and p120Cat bound to all proteins (Figure 5C). Consistent with our previous findings, Afadin and NUFIP2 showed a preference for proteins with the PTPRK-D2 domain, which is particularly evident by supernatant depletion (Figure 5C). In contrast, RAPGEF6 bound equally to both PTPRK domains (Figure 5C). In dephosphorylation assays, proteins with the PTPRM D1 were used at a 3-fold higher concentration than PTPRK D1 domains to compensate for their lower activity (Figure 5—figure supplement 1E). Strikingly, the PTPRK-D2 domain is sufficient to recruit Afadin for dephosphorylation by PTPRM-D1 (Figure 5D). In contrast, p120Cat is dephosphorylated by all domains, based on its presence in the associated supernatants (Figure 5D). Consistent with our previous findings, Paxillin is not dephosphorylated by any PTPRK or PTPRM combinations (Figure 5D). Together, these data demonstrate that PTPRK and PTPRM can directly and selectively dephosphorylate substrates, and that the D2 pseudophosphatase domain is necessary and sufficient for recruitment of the PTPRK-specific substrate, Afadin.

A role for RPTP pseudophosphatase domains in substrate recognition has been proposed, however, the mechanism remains elusive. Structural studies on other RPTP D2 domains show a canonical PTP fold (Barr et al., 2009; Nam et al., 1999; Nam et al., 2005) and resemble substrate traps due to amino acid variation in key catalytic motifs. For example, the LAR (PTPRF) D2 domain could be converted to an active PTP by just two mutations (Nam et al., 1999). We were unable to deplete Afadin from the PTPRK D2 domain with vanadate or dephosphorylation of cell lysates, suggesting binding is not mediated by phosphotyrosine (Figure 5—figure supplement 2A and B). We next attempted to reactivate the PTPRK D2 domain by reintroducing canonical sequences to the WPD loop, PTP signature motif and Q loop (Figure 5—figure supplement 2C; Andersen et al., 2001). Using a pNPP assay, we found no impact of the mutations on D2 domain activity (Figure 5—figure supplement 2D), similar to recent failed attempts to reactivate the PTPRE D2 domain (Lountos et al., 2018). Importantly, the D2 domain mutations did not abrogate binding to several interactors (Figure 5—figure supplement 2E). The catalytic cysteine, which forms a phosphocysteine intermediate in PTP D1 domains (Pannifer et al., 1998), is conserved in most RPTP D2 domains (Andersen et al., 2001). However, the CD45 (PTPRC) D2 domain structure shows that this key cysteine is occluded when compared to that of the D1 (Figure 5—figure supplement 2F). We generated a homology model for the PTPRK D2 domain based on PTPRE, and found that the surface charge surrounding the putative active site significantly diverges from that of the D1 domain (Figure 5—figure supplement 2G). These data suggest the D2 domain substrate recognition mechanism does not require substrate phosphorylation, which is consistent with our earlier findings (Figure 2H and I) as well as PTPRK D2 domain structural and sequence features.

PTPRK dephosphorylates p120Cat-pY228 and -pY904 in MCF10A cells

The Phosphosite plus database includes 17 frequently phosphorylated Human p120Cat tyrosine residues that have been identified by mass spectrometry (Hornbeck et al., 2015). By the same criteria, the larger protein Afadin is phosphorylated on only five tyrosine residues (Hornbeck et al., 2015). This difference might explain why PTPRK completely dephosphorylates most of the Afadin present in lysates, but only a fraction of p120Cat (Figure 5B). Therefore, our dephosphorylation assays are likely to be quite conservative, particularly for proteins with many phosphosites. Our phosphoproteomics data revealed hyperphosphorylation of p120Cat-Y174, -Y228, -Y865 and -Y904 in PTPRK KO cells, suggesting these could be direct targets for PTPRK. Antibodies were available to detect phosphorylated p120Cat-Y228 and -Y904. To determine whether these sites could be directly dephosphorylated we incubated pervanadate lysates with recombinant protein domains and immunoblotted for specific phosphosites. In all cases, PTP domains did not dephosphorylate EGFR-pY1068 or Paxillin-pY118 (Figure 6A and Figure 6—figure supplement 1A and B). In contrast, PTPRK-D1 and ICD, but not the catalytically inactive PTPRK-C1089S (Figure 6A) or pervanadate-inhibited PTPRK ICD (Figure 6—figure supplement 1A), almost completely dephosphorylated both p120Cat-pY228 and -pY904 sites. PTPRM also dephosphorylated both sites (Figure 6—figure supplement 1B). Whilst these p120Cat sites are efficiently dephosphorylated by PTPRK, only a small fraction of p120Cat undergoes complete dephosphorylation (Figure 5B). Combined with the observation that p120Cat-pY257 levels were unchanged in PTPRK KO cells by phosphoproteomics (Figure 3—source data 1) our data are consistent with PTPRK site selectivity, at least for p120Cat.

Figure 6 with 1 supplement see all
PTPRK dephosphorylates p120Cat Y228 and Y904 in MCF10A cells.

(A) Pervanadate-treated MCF10A lysates were incubated with and without the indicated recombinant PTPRK-D1, PTPRK-ICD or PTPRK-C1089S-ICD for 1.5 hr at 4°C, prior to immunoblot analysis. (B–C) Lysates from confluent wildtype and PTPRK KO MCF10As were analyzed by immunoblot and quantified by densitometry. Error bars denote ±SEM (n ≥ 3). Unpaired, two-tailed t test: *p<0.05, **p<0.005. (D) Wildtype or PTPRK KO MCF10As, with stably-integrated doxycycline-inducible tGFP, PTPRK or PTPRK-C1089S, were cultured for 6 days with indicated concentrations of doxycycline then lysed and subjected to immunoblot analysis. (E) Densitometric quantification of p120Cat phosphorylation normalized against total p120Cat. Error bars denote ±SEM (n = 5). Two-way ANOVA (Tukey’s multiple comparisons test): *p<0.005**, p<0.005, ***p<0.0005. See also Figure 6—figure supplement 1.

https://doi.org/10.7554/eLife.44597.020

Immunoblotting confirms that p120Cat-pY228 and -pY904 are increased on average 3–4-fold in confluent PTPRK KO cells compared to wildtype, whereas Paxillin-pY118 is unchanged, consistent with our phosphoproteomics results (n = 4; Figure 6B and C; Figure 3—source data 2). We next used the site-specific p120Cat phosphoantibodies to assess whether the direct dephosphorylation of putative substrates observed in vitro translated to an intact cellular context. Doxycycline-induction of PTPRK, but not the C1089S mutant, in PTPRK KO cells reproducibly and dose-dependently reduced p120Cat-pY228 and -pY904 levels, without affecting total p120Cat (n = 5; Figure 6D and E). Conversely, reintroduction of PTPRK did not affect Paxillin-pY118. These results suggest PTPRK is an active and selective tyrosine phosphatase for p120Cat in confluent MCF10A cells.

PTPRK promotes junction integrity in epithelial cells

We have demonstrated that Afadin, PARD3, PKP3, PKP4, and p120Cat are high confidence substrates for PTPRK, with PLEKHA6, MAP4K4, PKP2, KIAA1217, ABLIM3 and Girdin also being good candidates. Because these proteins are linked by roles in cell-cell junction organization, we sought to determine the impact of PTPRK loss on MCF10A morphology. Wildtype and PTPRK KO cells displayed signaling differences by phosphoproteomics at 24 hr after media change (Figure 3B). We therefore used the same conditions to investigate junctional integrity of confluent cells. To this end, wildtype and PTPRK KO cells grown on transwell filters were analyzed by electron microscopy. Wildtype cells were more closely packed and organized than PTPRK KO cells, which exhibited large gaps between cells (Figure 7A). Moreover, we observed a striking reduction in cell height in PTPRK KO cells (Figure 7A (inset) and 7B). We further investigated junctional integrity by measuring the transepithelial electrical resistance (TEER) and FITC dextran permeability of cells grown on transwell filters. PTPRK KO cells exhibited a ~ 50% reduction in TEER and a small but significant increase in FITC-dextran permeability compared to wildtype cells indicating a leakier monolayer (Figure 7—figure supplement 1A–B). TEER measurements were partially rescued by reintroduction of PTPRK, but not a catalytically inactive mutant (Figure 7C). Consistent with this altered organization, immunostained PTPRK KO cells grown on coverslips displayed a ~ 20% decrease in the intensity of F-actin, the AJ protein E-Cadherin, the desmosomal protein Desmoglein 3 (DSG3) and the PTPRK substrate p120Cat (Figure 7—figure supplement 1C–F). The junctional markers also displayed reduced colocalization with F-actin (Figure 7—figure supplement 1G–H). However, the levels of these junctional proteins were unaffected by PTPRK loss (Figure 6B and Figure 7—figure supplement 1I). Reintroduction of PTPRK or PTPRK-C1089S was able to partially rescue E-Cadherin intensity (Figure 7D and Figure 7—figure supplement 2A), however, catalytic activity was required to rescue F-actin intensity (Figure 7D–E). In line with this, rescue of E-Cadherin and F-actin colocalization requires PTPRK D1 domain activity, suggesting PTPRK substrate hyperphosphorylation contributes to impaired junctional integrity.

Figure 7 with 2 supplements see all
PTPRK promotes junction integrity and organization in epithelial cells.

(A) Wildtype (Left) and PTPRK KO (Right) MCF10As were cultured on transwell filters before being fixed and prepared for conventional electron microscopy (EM). Scale bar = 5 µm. (B) Quantification of cell height relative to transwell filter. Three measurements per image were averaged. Each data point relates to one EM image. Error bars denote ±SEM. Unpaired, two tailed t test ***p<0.0005. (C) Stable PTPRK KO MCF10As were grown to confluence with or without 250 ng/ml doxycycline on 0.4 µm transwell filters prior to TEER analysis. Error bars denote ±SEM (n = 3). Two-way ANOVA (Sidak's multiple comparisons test): *p<0.05. (D) Confluent PTPRK KO MCF10As, with stably-integrated doxycycline-inducible PTPRK or PTPRK-C1089S, were cultured for 6 days with or without 250 ng/ml doxycycline then fixed and stained for E-Cadherin and F-actin. A representative confocal microscopy image is shown. Scale bar = 20 µm. (E) Quantification of relative F-actin staining intensity. 10 random fields/replicate were averaged. Error bars denote ±SEM (n ≥ 3). Two-way ANOVA (Sidak's multiple comparisons test): *p<0.05 (F) Quantification of colocalization (Pearson coefficient) between E-Cadherin and F-actin staining. 10 random fields/biological replicate were averaged. Error bars denote ±SEM (n = 3). Two-way ANOVA (Sidak's multiple comparisons test): *p<0.05. See also Figure 7—figure supplement 1.

https://doi.org/10.7554/eLife.44597.023

It has previously been reported that shRNAs targeting PTPRK in MCF10A cells perturbs their morphogenesis in 3D culture (Ramesh et al., 2015). We find PTPRK KO cells mostly form normal acini (Figure 8 and Figure 8—figure supplement 1A); however,~20% exhibited a branched or protrusive morphology after 14 days in culture (Figure 8B), resembling the previously described invasive behavior observed upon combined EGFR and Src overexpression in MCF10A cells (Dimri et al., 2007). When we collected intact spheroids for immunostaining we found normal apical polarization of the Golgi (Figure 8C). However, PTPRK KO spheroids were significantly larger, by diameter, than wildtype (Figure 8D), despite similar proliferation rates of subconfluent cells in 2D (Figure 8—figure supplement 1B). Overall, our results support a role for PTPRK in promoting cell-cell junctions and repressing invasive behavior, probably through recruitment and dephosphorylation of several cell junction organizers.

Figure 8 with 1 supplement see all
PTPRK promotes organization in epithelial cells.

(A) Phase contrast images of wildtype and PTPRK KO. MCF10A spheroids after 14 day culture in Matrigel. Scale bar = 200 µm. (B) Frequency of aberrant acini observed in six independent wells each of wildtype and PTPRK KO MCF10A spheroids. Unpaired, two-tailed t test: *p<0.05. (C) Representative images of MCF10A spheroids stained for the Golgi marker GM130, F-actin and nuclei (Hoechst), after removal from Matrigel. Scale bar = 20 µm. (D) Circles were traced over cross sections, based on the Hoechst channel, for a total of 563 WT and 551 PTPRK KO immunostained spheroids from three entire slides per genotype and diameters calculated in Zen Pro. Unpaired, two-tailed t test: ***p<0.0005. See also Figure 8—figure supplement 1.

https://doi.org/10.7554/eLife.44597.027

Discussion

We have used unbiased approaches to identify five high confidence substrates of the cell-contact sensing receptor PTPRK, including Afadin, PARD3, p120Cat, PKP3 and PKP4. These substrates are linked to cell-cell junction organization, which is perturbed when PTPRK is deleted. Importantly, our findings demonstrate the substrate selectivity of this receptor, which requires both its active and inactive PTP domains. We also identify PTPRK as a key mediator of adhesive signaling. Our conclusions have implications not only for understanding PTP biology and cell-cell junction phosphoregulation, but also provide molecular insight into how PTPRK might function as a tumor suppressor.

Cross-referencing the PTPRK interactome with the PTPRK-dependent tyrosine phosphoproteome enabled us to identify candidate substrates to assay for cellular interactions and direct dephosphorylation. Substrate-trapping methods in combination with mass spectrometry are commonly used to identify PTP substrates (Blanchetot et al., 2005). We used two mutants affecting the WPD catalytic motif (D1057A) and catalytic cysteine within the PTP signature motif (C1089S) and found enrichment of distinct proteins on each. Using both Hs27 and MCF10A lysates, MAP4K4 and RAPGEF6 were enriched on the D1057A trap. Both were partially competed from traps with the phosphate mimetic vanadate, suggesting phosphorylation-dependent interaction. However, we could not validate RAPGEF6 or MAP4K4 as PTPRK substrates by in vitro dephosphorylation or phosphoproteomics, perhaps reflecting a limitation to the sensitivity or selectivity of our assays. Interestingly, these proteins were recently linked to mechanotransduction and hippo signaling, along with the PTPRK interactor MINK1 (Meng et al., 2018). An interesting future line of research will be to determine whether PTPRK is an upstream regulator of this new mechanotransduction pathway.

The cell junction organizers PARD3, Afadin and PLEKHA6 were all trapped by the C1089S mutant. Our immunoblots also highlighted phosphorylation-dependent enrichment of p120Cat and PKP4 on this trap. These five proteins were subsequently found to be hyperphosphorylated in PTPRK KO cells, suggesting that the C1089S mutant was effective in identifying substrates. However, we also found hyperphosphorylation of other PTPRK-binding partners in KO cells, indicating the traps alone were too restrictive in identifying substrates. Indeed, the PTPRK pseudophosphatase D2 domain was sufficient for substrate recognition, which may have masked the effect of the substrate traps, particularly as we have shown that D2 domain binding to most proteins is independent of tyrosine phosphorylation. By considering the entire PTPRK interactome, we could include the armadillo family proteins PKP3, PKP4 and p120Cat as substrates. Our criteria were quite conservative, and it is likely that ABLIM3, PLEKHA6, Girdin, KIAA1217 and PKP2 are also substrates, all of which are also linked to junction organization (Gallegos et al., 2016; Guo et al., 2014). Furthermore, we cannot rule out the existence of additional PTPRK substrates, for example, that are expressed in different cellular contexts, particularly as we observed divergent interactomes between epithelial and fibroblast cells.

Strikingly, most of the candidate PTPRK substrates identified here have orthologs in Drosophila, yet the R2B receptor family first appears in chordates (Chen et al., 2017). This suggests that rather than co-evolving with its substrates, PTPRK regulates pre-established functional protein complexes. In this way, PTPRK would have introduced new regulation, and perhaps function, to existing signaling networks for chordate and vertebrate-specific organization. Indeed, there are genetic links between orthologs for RAPGEF6, PARD3 and Afadin in the regulation of Drosophila AJ formation (Bonello et al., 2018). Furthermore, PARD3 and p120Cat Drosophila orthologs have been linked to the control of E-Cadherin internalization and recycling (Bulgakova and Brown, 2016). Several PTPRK substrates belong to the δ-catenin family, which undergoes significant expansion from one gene in Drosophila to seven in vertebrates (Carnahan et al., 2010). We did not detect ACRVF, PKP1 or δ-catenin (CTNND2) in MCF10A total proteomes (Figure 3—source data 1); however, these might be additional R2B family substrates in other cell types, such as neurons (Paffenholz and Franke, 1997). PKP2 was an interactor and hyperphosphorylated in PTPRK KO cells, but its dephosphorylation was not assessed. PKP3 has been proposed to promote the stability of desmosomes upon overexpression (Gurjar et al., 2018). PKP4 is targeted to both adherens junctions and desmosomes, but its role is less well understood (Hatzfeld et al., 2003). Our finding that PTPRK promotes junctional integrity raises the possibility that dephosphorylation of substrates, such as p120Cat, would stabilize cadherin-based junctional assemblies. Interestingly, our ultrastructural analysis showed that PTPRK KO cells have leakier junctions and are shorter and less organized. This is reminiscent of the proposed role of p120Cat in controlling epithelial cell lateral domain expansion and shape maturation by balancing junctional contractility and maturation through regulation of E-Cadherin and RhoA (Yu et al., 2016), which reportedly depends on p120Cat tyrosine phosphorylation status (Castaño et al., 2007; Davis et al., 2003; Fukumoto et al., 2008). Indeed, we show that PTPRK dephosphorylates p120Cat in cells, and that PTPRK phosphatase activity is necessary to rescue junctional deficits.

Afadin appears to be a unique PTPRK substrate; it was not dephosphorylated by the very closely related PTPRM and it had the highest fold increase in tyrosine phosphorylation in PTPRK KO cells. Strikingly, this specificity is determined in large part by the PTPRK D2 pseudophosphatase domain, which was sufficient to recruit Afadin for dephosphorylation by the PTPRM D1 domain. This might reflect the greater identity between the PTPRK and PTPRM active D1 domains than the D2 domains (78% vs 73.6%). In line with this, we found little evidence for a PTPRK substrate consensus sequence other than a bias against basic residues immediately adjacent to the phosphotyrosine site, similar to previous reports for other PTPs (Barr et al., 2009). Several RPTPs have tandem intracellular PTP domains and the precise function of the inactive D2 domains remain to be determined (Tonks, 2006). The Janus kinases have a similar tandem arrangement where a pseudokinase domain regulates kinase activity (Babon et al., 2014). Indeed, regulation of the PTP D1 by D2 domains has been suggested for several RPTPs (Toledano-Katchalski et al., 2003). We do observe a three-fold reduction in PTPRK ICD enzyme activity compared to the D1 domain alone. However, when free D2 domain was added to free D1 domain, we saw no impact on activity. Instead, we find a key role for the pseudophosphatase domain in substrate recognition, similar to findings for CD45/PTPRC (Nam et al., 2005). We further show that unlike LAR (Nam et al., 1999), the PTPRK D2 domain could not easily be reactivated by mutation. Additionally, we rule out a role for the D2 domain in phosphotyrosine recognition using dephosphorylated lysates, vanadate competition and a PTPRK homology model. Several previous reports have shown that wildtype PTPs can interact with substrates, which are presumably in a dephosphorylated state (Chen et al., 2006; Lee and Bennett, 2013; Timms et al., 1998). Thus, PTPRK might serve as a scaffold for dephosphorylated proteins either by recruiting non-phosphorylated proteins, or by dephosphorylating already phosphorylated proteins upon recruitment. It is likely that the combination of recognition and dephosphorylation is important for full PTPRK function. Determining the spatiotemporal dynamics of PTPRK protein recruitment will be an important next step.

PTPRK and PTPRM both dephosphorylated PARD3, p120Cat, PKP3 and PKP4 in lysates. Despite this, hyperphosphorylation of sites on each of these proteins were found in PTPRK KO cells, indicating that PTPRM cannot fully compensate for PTPRK loss. This could be due to lower PTPRM expression levels in MCF10A cells, possible differences in site selectivity or its intrinsically lower catalytic activity (this study and Barr et al., 2009). Vertebrate genomes all encode at least 4 R2B family members, with distinct expression profiles (Figure 1—figure supplement 1A). For example, by in situ hybridization the receptors display divergent expression patterns in the adult mouse cerebellum (Besco et al., 2004). Assuming they are regulated similarly by cell-cell contact, our results indicate that receptor expression patterns will determine subtly distinct responses to cell contact.

Several phosphosites that are regulated by PTPRK have been characterized previously. p120Cat-Y228 is phosphorylated in response to EGFR and a construct with N terminal phosphorylation-deficient mutations (including Y228F) is capable of rescuing adhesion phenotypes caused by p120cat deletion (Mariner et al., 2004). In contrast, a phosphomimetic p120Cat -Y228E mutant increased recruitment of RhoA (Castaño et al., 2007). Afadin Y1237 phosphorylation, the rat equivalent of Human Afadin Y1230, has been shown to mediate recruitment of SHP2, implicating it in Ras-Mitogen activated protein kinase signaling (Nakata et al., 2007). This supports the role of PTPRK-mediated dephosphorylation of this site in tumor suppression.

PTPRK is the only R2B family member implicated by transposon-based mouse forward genetics in the progression of several cancers (March et al., 2011; Starr et al., 2009) and has been proposed to function as a tumor suppressor. Moreover, specific gene fusions result in its promoter driving the expression of oncogenic RSPO3 in a subset of colorectal cancers (Seshagiri et al., 2012). This is consistent with PTPRK being the predominant R2B receptor expressed in the mouse intestinal epithelium (Haber et al., 2017). Our findings of abrogated junction organization, spheroid overgrowth and invasive behavior in PTPRK-deficient cells support its role as a tumor suppressor. Several of the PTPRK substrates identified here have been linked to cancer, including PARD3 loss-of-function in invasion (de la Rosa et al., 2017), and oncogenic and tumor suppressive roles for p120Cat (Schackmann et al., 2013). Thus, their combined dysregulation could contribute to pathological phenotypes in a PTPRK mutant setting. Compromised epithelial barrier integrity is also linked to inflammatory bowel disease susceptibility; therefore, PTPRK SNPs linked to celiac disease should be investigated (Trynka et al., 2011). Our analysis of PTPRK KO cells showed downregulation of epithelial markers such as Keratin14, and upregulation of several mesenchymal markers such as vitronectin (VTN; Figure 3C and Figure 3—source data 1). PTPRK is a TGFβ target gene (Wang et al., 2005), and our data suggest it functions to suppress epithelial to mesenchymal transition (EMT), indicating a negative feedback role that could lead to pathological effects if perturbed (Brabletz et al., 2018).

Finally, our results provide evidence for cross-talk between PTPRK and growth factor signaling. Although PTPRK does not dephosphorylate EGFR in our assays, consistent with previous peptide assays (Barr et al., 2009), we did observe an interaction by BioID. Indeed, EGFR family interactions with R2B receptors have been reported (Yao et al., 2017). Growth factor stimulation leads to PTPRK tyrosine phosphorylation (Batth et al., 2018; Reddy et al., 2016) and it has been suggested that RTK-induced PTP inhibition by oxidation impacts cellular signaling (Reynolds et al., 2003). PTPs are well-placed to fine-tune and tailor responses to particular cellular contexts. Several PTPRK substrates are phosphorylated in a Src-dependent manner (Reddy et al., 2016). PTPRK might therefore provide feedback in the context of cell contact by dephosphorylating its substrates to promote junctional integrity. Indeed, overexpression of v-Src in epithelial cells leads to junction disassembly and EMT (Woodcock et al., 2009). Thus, such PTPs could act as interpreters of the cellular context. Interestingly, an analogous role for the contact-sensing RTK EphA2 was recently reported (Stallaert et al., 2018).

In summary, by defining the substrate repertoire of human PTPRK, we reveal mechanistic insight into its putative tumor suppressor role through its control of cell-cell junctions and suppression of EMT. Our study raises new questions about the phosphoregulation of junctional proteins and implicates PTPRK as a direct sensor and mediator of cell adhesion. We show that the PTPRK D2 domain is critical for substrate recognition, yet binds proteins independently of phosphorylation status. It will be of great interest to determine whether these findings hold true for other RPTPs. In addition, it is unknown whether the R2B receptor extracellular regions, which were previously described as spacer clamps (Aricescu et al., 2007), affect phosphatase activity or substrate recruitment. Finally, we show that PTPRK, like other PTPs (Li et al., 2013), does not recognize a peptide consensus sequence, unlike certain serine/threonine phosphatases (Shi, 2009), highlighting the need for the approach we have taken. Thus, we provide a framework for systematically identifying RPTP substrates, which in turn will advance our knowledge of these poorly characterized, yet important enzymes.

Materials and methods

Key resources table
Reagent type
(species) or
resource
DesignationSource or
reference
IdentifiersAdditional
information
Gene (Homo sapiens)PTPRKENSEMBL: ENST00000368213.9
Cell line (H. sapiens)MCF10AATCCCRL-10317
Cell line (H. sapiens)HEK293TD RonN/A
Cell line (H. sapiens)HEK293Sigma (ECACC)85120602-1VL
Cell line (H. sapiens)Hs27 FibroblastsSigma (ECACC)94041901-1VL
Cell line (H. sapiens)MCF10A PTPRK KO A4This studyCRISPR/Cas9 and
clonal selection
Cell line (H. sapiens)MCF10A PTPRK KO E3This studyCRISPR/Cas9 and
clonal selection
Cell line (H. sapiens)MCF10A PTPRK KO H1This studyCRISPR/Cas9 and
clonal selection
Cell line (H. sapiens)MCF10A PTPRK KO pooledThis study
Transfected
construct (H. sapiens)
MCF10A PTPRK KO pooled.tGFPThis studyLentivirally transduced
stable cell line
Transfected
construct (H. sapiens)
MCF10A PTPRK
KO pooled.tGFP.P2A.PTPRK
This studyLentivirally transduced
stable cell line
Transfected
construct (H. sapiens)
MCF10A PTPRK KO pooled.tGFP.P2A.PTPRK.C1089SThis studyLentivirally transduced
stable cell line
Transfected
construct (H. sapiens)
MCF10A.tGFPThis studyLentivirally transduced
stable cell line
Transfected
construct (H. sapiens)
MCF10A.tGFP.P2A.PTPRK.ECD-TMD.BirA*-FlagThis studyLentivirally transduced
stable cell line
Transfected
construct (H. sapiens)
MCF10A.tGFP.P2A.PTPRK.C1089S.BirA*-FlagThis studyLentivirally transduced
stable cell line
Transfected
construct (H. sapiens)
MCF10A PTPRK KO pooled.nuclear mAppleThis studyLentivirally transduced
stable cell line
Transfected
construct (H. sapiens)
MCF10A.nuclear mAppleThis studyLentivirally transduced
stable cell line
AntibodyRabbit monoclonal anti-PTPRKThis study2 .G6Western blot: 1:1000
AntibodyRabbit monoclonal anti-PTPRKThis study2 .H4Western blot: 1:1000
AntibodyRabbit monoclonal anti-PTPRKThis study2 .H5Western blot: 1:1000
AntibodyRabbit monoclonal anti-PTPRKThis study1 .F4FACS (1:200)
and Immunofluorescence
(IF; 1:200)
AntibodyMouse anti-PTPRKSanta Cruz BiotechnologyCat#Sc- 374315Western blot: 1:1000 (note: we did not observe any specific signal for PTPRK with this antibody)
AntibodyRabbit anti-PARD3SigmaCat#HPA030443 (lot: C105765)Western blot: 1:1000
AntibodyRabbit anti-PARD3Merck MilliporeCat#07–330Western blot: 1:1000
AntibodyMouse anti-RAPGEF6Santa Cruz
Biotechnology
Cat#sc-398642 (F-8)Western blot: 1:1000
AntibodyMouse anti-AfadinBD Transduction LabsCat#610732Western blot: 1:1000
AntibodyMouse anti-DLG5Santa Cruz
Biotechnology
Cat#SC374594 (A-11)Western blot: 1:1000
AntibodyMouse anti-PTPN14R and D SystemsCat#MAB4458Western blot: 1:1000
AntibodyMouse anti-E-CadherinBD Transduction
Labs
Cat#610181Western blot:
1:1000 IF: 1:100
AntibodyRabbit anti-b-CateninCell Signaling
Technology
Cat#9562SWestern blot: 1:1000
AntibodyRabbit anti-Phospho-EGFR (Y1068)Cell Signaling
Technology
Cat#3777SWestern blot: 1:1000
AntibodyRabbit anti-EGFRCell Signaling
Technology
Cat#4267SWestern blot: 1:1000
AntibodyRabbit anti-phospho-tyrosine(P-Tyr-1000)Cell Signaling
Technology
Cat#8954Western blot: 1:2000
AntibodyRabbit anti-MAP4K4Cell Signaling
Technology
Cat#5146Western blot: 1:1000
AntibodyRabbit anti-NUFIP2Bethyl
Laboratories, Inc
Cat#A301-600AWestern blot: 1:1000
AntibodyRabbit anti-FMRP1ThermoFisher
Scientific
Cat#MA5-15499Western blot: 1:1000
AntibodyRabbit anti-MINK1/MAP4K6ThermoFisher
Scientific
Cat#PA5-28901Western blot: 1:1000
AntibodyRabbit anti-PKP4Bethyl
Laboratories, Inc
Cat#A304-649AWestern blot: 1:1000
AntibodyMouse anti-P120 cateninBD Transduction
Laboratories
Cat#610133Western blot:
1:1000 IF: 1:100
AntibodyMouse anti-GM130BD Transduction
Laboratories
Cat#610822Western blot: 1:1000
AntibodyRabbit anti-STAT3Cell Signaling
Technology
Cat#4904SWestern blot: 1:1000
AntibodyRabbit anti-PaxillinCell Signaling
Technology
Cat#12065 (D9G12)Western blot: 1:1000
AntibodyMouse anti-Tubulin (Alpha)SigmaCat#T6199Western blot: 1:1000
AntibodyMouse anti-PTPRMSanta CruzCat#sc-56959Western blot: 1:1000
AntibodyRabbit anti-PKP3AbcamCat#AB109441Western blot: 1:10000
AntibodyRabbit-anti-ABLIM3SigmaCat#HPA003245Western blot: 1:1000
AntibodyRabbit-Anti-ZO2ThermoFisher
Scientific
Cat#711400Western blot: 1:1000
AntibodyRabbit-anti-Phospho-P120 catenin (Y904)Cell Signaling
Technology
Cat#2910Western blot: 1:1000
AntibodyRabbit-anti-Phospho-P120 catenin (Y228)Cell Signaling
Technology
Cat#2911Western blot: 1:1000
AntibodyRabbit polyclonal anti-Phospho-Paxillin (Y118)Cell Signaling
Technology
Cat#2541Western blot: 1:1000
AntibodyRabbit-anti-b-ActinSIGMACat#A2066Western blot: 1:1000
AntibodyMouse-anti-DSG3Bio-RadCat#MCA2273TWestern blot: 1:5000
AntibodyHRP conjugated-Donkey
anti-Rabbit IgG
Jackson
Immuno-Research
Cat#711-035-152Western blot: 1:5000
AntibodyHRP conjugated- Donkey anti-Mouse IgGJackson
Immuno-Research
Cat#711-035-152Western blot: 1:5000
AntibodyHRP conjugated- Mouse anti-Rabbit IgG (Conformation specific)Cell Signaling
Technology
Cat#5127SWestern blot: 1:2000
AntibodyAtto-488 Goat Anti-mouse IgGSigmaCat#62197IF: 1:400
AntibodyAtto-488 Goat Anti-mouse IgGSigmaCat#62197IF: 1:400
AntibodyAlexa Fluor-647 Goat Anti Rabbit IgGJackson
Immuno-Research
Cat#111-605-003IF: 1:400
Recombinant
DNA reagent
pCW57.tGFP.P2A.MCSAddgeneCat#71783
Recombinant
DNA reagent
pRK.HA.PTPRK.flagGenentechCorresponds to
Uniprot identifier:
Q15262-3
Recombinant
DNA reagent
pRK.PTPRK(1-752).IgG1Genentech
Recombinant
DNA reagent
pET15bJ. Deane
Recombinant
DNA reagent
pSP.Cas9.(BB).eGFPD Ron
Recombinant
DNA reagent
pMD2.GAddgeneCat#12259
Recombinant DNA reagentpsPAX2AddgeneCat#12260
Recombinant
DNA reagent
pLenti-puroAddgeneCat#39481
Recombinant
DNA reagent
PTPRK-BirA-R118G-FlagA-C Gingras
Recombinant
DNA reagent
pCW57.tGFP.P2A.PTPRKThis study
Recombinant
DNA reagent
pCW57.tGFP.P2A.PTPRK.C1089SThis study
Recombinant
DNA reagent
pCW57.tGFP.P2A.PTPRK(1-785).BirA-R118G.FlagThis study
Recombinant
DNA reagent
pCW57.tGFP.P2A.PTPRK.C1089S.BirA-R118G.FlagThis study
Recombinant
DNA reagent
pET15b.His.TEV.AviThis study
Recombinant
DNA reagent
pET15b.His.TEV.Avi.PTPRK.ICDThis study
Recombinant
DNA reagent
pET15b.His.TEV.Avi.PTPRK.ICD.D1057AThis study
Recombinant
DNA reagent
pET15b.His.TEV.Avi.PTPRK.ICD.C1089SThis study
Recombinant
DNA reagent
pET15b.His.TEV.Avi.PTPRK.D1This study
Recombinant
DNA reagent
pET15b.His.TEV.Avi.PTPRK.D2This study
Recombinant
DNA reagent
pET15b.His.TEV.Avi.
PTPRK.D2.triple
This studyMutations: A1346P,
S1347D, L1384S,
E1427Q, A1428T
Recombinant
DNA reagent
pET15b.His.TEV.Avi.PTPRM.ICDThis study
Recombinant
DNA reagent
pET15b.His.TEV.Avi.PTPRM.D1This study
Recombinant
DNA reagent
pET15b.His.TEV.Avi. PTPRK-D1_K-D2.This study
Recombinant
DNA reagent
pET15b.His.TEV.Avi.PTPRM-D1_M-D2This study
Recombinant
DNA reagent
pET15b.His.TEV.Avi.PTPRK-D1_M-D2.This study
Recombinant
DNA reagent
pET15b.His.TEV.Avi.PTPRM-D1_K-D2.This study
Recombinant
DNA reagent
pET15b.His.TEV.Avi.Src.sbSH2This study
Recombinant
DNA reagent
pET15b.His.TEV.Avi.Grb2.sbSH2This study
Recombinant
DNA reagent
pSP.Cas9.PTPRK.sgRNA1This study
Recombinant
DNA reagent
pSP.Cas9.PTPRK.sgRNA2This study
Sequence-based reagentON-TARGETplus Human PTPRK siRNADharmacon,
GE Healthcare
Cat#J-004204–06
Sequence-
based reagent
ON-TARGETplus Non-targeting pool siRNADharmacon,
GE Healthcare
Cat#D-001810-10-05
Sequence-
based reagent
PTPRK CRISPR, BbsI.PTPRKgRNA1.FwdSIGMACACCGCATGGATACGACTGCGGCGG
Sequence-
based reagent
PTPRK CRISPR, BbsI.PTPRKgRNA1.RevSIGMAAAACCCGCCGCAGTCGTATCCATGC
Sequence-
based reagent
PTPRK CRISPR, BbsI.PTPRKgRNA2.FwdSIGMACACCGATCTCGGGTGGTAGATAATG
Sequence-
based reagent
PTPRK CRISPR, BbsI.PTPRKgRNA2.RevSIGMAAAACCATTATCTACCACCCGAGATC
Sequence-
based reagent
TaqMan probe: Hs02338565_gH (RPL19)Thermo Fisher
Scientific
Cat#4331182
Sequence-
based reagent
TaqMan probe: Hs00267788_m1 (PTPRK)Thermo Fisher
Scientific
Cat#4331182
Sequence-
based reagent
TaqMan probe: Hs00267809_m1 (PTPRM)Thermo Fisher
Scientific
Cat#4331182
Sequence-
based reagent
TaqMan probe: Hs00179247_m1 (PTPRT)Thermo Fisher
Scientific
Cat#4331182
Sequence-
based reagent
TaqMan probe: Hs00963911_m1 (PTPRU)Thermo Fisher
Scientific
Cat#4351372
Peptide,
recombinant
protein
DADE-pTyr-LIPQQG-
phospho-peptide
Cambridge
Research
Biochemicals
Cat#crb1000746
Peptide,
recombinant protein
END-pTyr-INASL-phospho-peptideCambridge
Research
Biochemicals
Cat#crb1000745
Peptide,
recombinant protein
CatalaseSigmaCat#C134514
Peptide,
recombinant protein
Cholera ToxinSigmaCat#C-8052
Peptide,
recombinant protein
InsulinSigmaCat#I-1882
Peptide,
recombinant protein
Epidermal Growth FactorPeprotechCat#AF-100-15-1MG
Peptide,
recombinant protein
Lysyl endopeptidase (LysC)WakoCat#129–02541
Peptide,
recombinant protein
Trypsin (proteomics grade)Thermo Fisher
Scientific
Cat#90058
Commercial
assay or kit
BIOMOL Green reagentENZOCat#BML-AK111-0250
Commercial
assay or kit
Phosphate standardENZOCat#BML-KI102-0001
Commercial
assay or kit
Q5 High-Fidelity DNA PolymeraseNew England
Biolabs
Cat#M0491S
Commercial
assay or kit
Phusion Hot Start II DNA polymeraseThermo Fisher
Scientific
Cat#F549L
Commercial
assay or kit
EZ-ECL substrateGeneflowCat#K1-0170
Commercial
assay or kit
NuPAGE MES
(2-ethanesulfonic acid) SDS running buffer
ThermoFisher
Scientific
Cat#NP0002
Commercial
assay or kit
InstantBlueExpedeonCat#ISB1L
Commercial
assay or kit
Phosphatase inhibitor cocktailRocheCat#04906845001
Commercial
assay or kit
TaqMan Universal Master Mix IIApplied BiosystemsCat#4440040
Commercial
assay or kit
MycoAlertTM PLUS Mycoplasma Detection KitLonza#LT07-705
Commercial
assay or kit
MycoProbe Mycoplasma Detection KitR and D Systems#CUL001B
Chemical
compound, drug
Hydrogen peroxideThermo Fisher
Scientific
Cat#H/1750/15
Chemical
compound, drug
Sodium orthovanadateAlfa AesarCat#J60191
Chemical
compound, drug
250 kDa-FITC-dextranSigmaCat#FD250S-100MG
Chemical
compound, drug
Para-Nitrophenol-phosphate (pNPP)New England BiolabsCat#P0757
Chemical
compound, drug
IPTGGeneronCat#GEN-S-02122
Chemical
compound, drug
D-biotinSigmaCat#B4639
Chemical
compound, drug
L-glutamineSigmaCat#G7513
Chemical
compound, drug
HydrocortisoneSigmaCat#H-0888
Chemical
compound, drug
PuromycinThermo Fisher
Scientific
Cat#A11138-03
Chemical
compound, drug
Phosphate free H2OThermo Fisher
Scientific
Cat#10977–035
Chemical
compound, drug
8M Guanidine HClThermo Fisher
Scientific
Cat#24115
Chemical
compound, drug
EPPS pH 8.5Alfa AesarCat#561296
Chemical
compound, drug
Trifluoroacetic Acid (TFA)Thermo Fisher
Scientific
Cat#28904
Chemical
compound, drug
AcetonitrileVWRCat#8364.290
Chemical
compound, drug
Sodium phosphate
dibasic (Na2HPO4)
Acros OrganicsCat#343811000
Chemical
compound, drug
NH4OHAcros OrganicsCat#460801000
Chemical
compound, drug
Methanol-free 16%
(w/v) paraformaldehyde (PFA)
Thermo Fisher
Scientific
Cat#28906
Software, algorithmMaxquantComputational
Systems
Biochemistry
Max Planck Institute
of Biochemistry
Software, algorithmPerseusComputational
Systems
Biochemistry
Max Planck Institute
of Biochemistry
Software, algorithmFIJI/ImageJLaboratory for
Optical and
Computational
Instrumentation
University of
Wisconsin-Madison
Software, algorithmZen BlueZeiss
Software, algorithmZen BlackZeiss
Software, algorithmGraphpadPrism
Software, algorithmChimeraUCSF
OtherHRP-conjugated
Streptavidin
Thermo Fisher
Scientific
Cat#434323
OtherSTABLE competent E. coliNEBCat#C3040I
OtherDH5alpha
competent E. coli
InvitrogenCat#18265017
OtherBL21 DE3 Rosetta E. coliJ DeaneN/A
OtherDMEMThermo Fisher
Scientific
Cat#41965–039
OtherHam's F-12SigmaCat#N4888
OtherHorse SerumThermo Fisher
Scientific
Cat#16050–122
OtherFibroblast growth
medium (FGM)
PromocellCat#C-23010
OtherFetal Bovine SerumSigmaCat#F7524-500ml
OtherTrypsin-EDTA solutionSigmaCat#T3924
OtherGeneJuice
transfection reagent
Merck MilliporeCat#70967–3
OtherEDTA-free
protease inhibitors
RocheCat#11836170001
OtherLipofectamine RNAiMaxInvitrogenCat#13778075
OtherOptiMEMThermo Fisher
Scientific
Cat#31985070
OtherLipofectamine LTXThermoFisher
Scientific
Cat#15338100
OtherProtein G agarose beadsMerck MilliporeCat#16–266
OtherNi-NTA agaroseQIAGENCat#1018244
OtherStreptavidin-coated
magnetic beads
New England
Biolabs
Cat#S1420S
OtherStreptavidin agaroseThermoFisher
Scientific
Cat#20357
OtherDMEM SILAC mediaThermo Fisher
Scientific
Cat#PI89985
OtherHam's F-12 SILAC mediaThermo Fisher
Scientific
Cat#88424
OtherHeavy Arginine + 10SigmaCat#608033–250 mg
 otherHeavy Lysine + 8SigmaCat#608041–100 mg
OtherProlineSigmaCat#P0380
OtherLight ArginineSigmaCat#A5006
OtherLight LysineSigmaCat#L5501
OtherHoechst 33342Thermo Fisher
Scientific
Cat#62249
OtherBODIPY 558/568 phalloidinInvitrogenCat#B3475IF: 1:400
OtherProLong Gold antifadeInvitrogenCat#P36934
OtherNormal Serum BlockBioLegendCat#927502
OtherMatrigelCorningCat#356231
Other0.2 mm nitrocellulose
membrane
GE HealthcareCat#15289804
Other0.4 mm pore size
Transwell filter
CorningCat#353095
Other24-well companion
plates
for Transwell filters
CorningCat#353504
OtherMillicell ERS-2
Volt/Ohm meter
Merck MilliporeCat#MERS00002
OtherSuperdex 200
16/600 column
GE HealthcareCat#28-9893-35
OtherSuperdex 75
16/600 column
GE HealthcareCat#28-9893-33
OtherUltracel-3K regenerated
cellulose centrifugal filter
Merck MilliporeCat#UFC900324
OtherUltracel-10 K
regenerated
cellulose centrifugal filter
Merck MilliporeCat#UFC901024
OtherUltracel-30 K regenerated
cellulose centrifugal filter
Merck MilliporeCat#UFC903024
OtherNuPAGE 4–12% Bis-Tris gelThermo Fisher
Scientific
Cat#NP0321BOX
Other1.5 ml low protein
binding centrifuge tubes
EppendorfCat#0030 108. 116
Other1cc/50 mg Sep-Pak
Vac tC18 cartridges
WatersCat#WAT054960,
Other1.5 ml Diagenode sonicator
tubes
DiagenodeCat#C30010010
Other5 ml low protein
binding centrifuge tubes
EppendorfCat#0030 108.302
Other2 ml low protein
binding centrifuge tubes
Thermo Fisher
Scientific
Cat#88379
OtherGraphite spin columnsThermo Fisher
Scientific
Cat#88302
OtherTitansphere Phos-TiO
Tips (200 ml/3 mg)
GL Sciences IncCat#5010–21311
Other18 mm x 18 mm,1.5
mm thick high-
performance coverslips
ZeissCat#474030-9000-000

Cells and cell culture

MCF10A cells were purchased directly from the American Type Culture Collection (ATCC; LGC Standards), and HEK293 and Hs27 cells were from the European Collection of Authenticated Cell Lines (ECACC; Sigma- Aldrich, UK). Cells were cultured in 75 cm2 vented tissue culture flasks and incubated at 37°C in a humidified 5% CO2 atmosphere and passaged, using trypsin-EDTA solution (Sigma-Aldrich), prior to reaching confluence, typically every 2–4 days depending on the cell line. MCF10A cells were grown in MCF10A growth media as described by the Brugge lab (Debnath et al., 2003) consisting of 50:50 DMEM (Thermo Fisher Scientific, UK)/Ham's F-12 (Sigma-Aldrich) containing 5% (v/v) horse serum (Thermo Fisher Scientific), 20 ng/ml EGF (Peprotech, UK), 0.5 μg/ml hydrocortisone (Sigma-Aldrich), 100 ng/ml cholera toxin (Sigma-Aldrich) 10 μg/ml insulin (Sigma-Aldrich). Hs27 cells were cultured in Fibroblast growth medium (Promocell, UK). HEK293 and HEK293T cells were cultured in DMEM containing 10% (v/v) FBS (Sigma-Aldrich), 2 mM L-glutamine (Sigma-Aldrich). Cell lines were tested for the presence of Mycoplasma using commercially available kits (see Key Resources table).

For SILAC analysis, MCF10A cells were cultured for 14 days in modified MCF10A growth media containing 50:50 SILAC DMEM (Thermo Fisher Scientific): SILAC F12 (Thermo Fisher Scientific), 5% (v/v) dialyzed horse serum and other supplements described above. For heavy labeling, 50 μg/ml lysine +8 (Sigma-Aldrich), 40 μg/ml arginine +10 (Sigma-Aldrich), 200 μg/ml proline (Sigma-Aldrich) were added. For light labeling, 50 μg/ml lysine (Sigma-Aldrich) and 40 μg/ml arginine (Sigma-Aldrich) were added. Isotopic labeling was assessed by mass spectrometry, following in-gel tryptic digest. At the start of each experiment heavy amino acid incorporation was ≥93%.

Plasmids and constructs

Amino acid (aa) numbering is based on the following sequences; PTPRK; UniProt ID: Q15262-3, PTPRM; UniProt ID: P28827-1. All point mutations were introduced by polymerase chain reaction (PCR) using either Q5 High-Fidelity DNA (New England Biolabs, UK) or Phusion Hot Start II DNA (Thermo Fisher Scientific) polymerases as per manufacturer’s protocol. The cDNA for the human PTPRK extracellular domain (ECD) of (aa 1–746) was synthesized with a C-terminal IgG1 tag fusion (GenScript, USA) and subcloned into the pRK vector (Genentech, USA). For transient mammalian expression, full-length human PTPRK coding expressing a N-terminal hemagglutinin (HA) tag and a C-terminal Flag tag was subcloned into the pRK vector. For stable integration with lentivirus infection, full length human PTPRK with and without a C-terminal BirA-R118G (BirA*)-Flag tag and truncated PTPRK (aa 1–785) with a C terminal BirA*-Flag tag were subcloned in-frame into pCW57.GFP.2A.MCS (a gift from Adam Karpf; #71783, Addgene, USA). For labeling nuclei, mApple with a C-terminal SV40 large T-antigen nuclear localization signal (PKKKRKV) was subcloned into the pLenti-puro vector (a gift from Ie-Ming Shih; #39481, Addgene). For bacterial expression, human coding sequences corresponding to PTPRK D1 (aa 864–1150) PTPRK D2 (aa 1150–1439), PTPRK intracellular domain (ICD; aa 864–1439), PTPRK ICD-C1089S, PTPRK ICD-D1057A, PTPRM D1(aa 877–1163), PTPRM ICD (aa 877–1452), PTPRK D1 (aa 864–1147)-BstBI-PTPRK D2 (aa 1150–1439), PTPRM D1 (aa 877–1159)-BstBI-PTPRM D2 (aa 1160–1452), PTPRK D1 (aa 864–1147)-BstBI-PTPRM D2 (aa 1160–1452), PTPRM D1 (aa 877–1159)-BstBI-PTPRK D2 (aa 1150–1439) were subcloned into a modified pET-15b bacterial expression vector in frame encoding an N-terminal His.TEV.AviTag (MGSSHHHHHHSSGVDLGTENLYFQGTGGLNDIFEAQKIEWHEGGGS).

The previously described Src and Grb2 mutant SH2 domains (Bian et al., 2016) were synthesized (Thermo Fisher Scientific) and subcloned into the same modified pET-15b bacterial expression vector by restriction digest.

Antibody production

New Zealand White (NZW) Rabbits were purchased from Western Oregon Rabbit Company (WORC). Rabbits were housed and immunized in Josman, LLC. The guideline of the animal care was under regulation of the Institutional Animal Care and User Committee (IACUC) requirement. The immunization protocol was approved by Roche IACUC and Genentech Laboratory Animal Resources. New Zealand White (NZW) rabbits were immunized with murine PTPRK protein. Rabbit anti-PTPRK mAb were generated from an antigen-specific single B cell cultivation and cloning platform based on a modified protocol (Seeber et al., 2014). PTPRK+/IgG + single B cells were directly sorted into culture plates using flow cytometry. The B cell culture supernatants were collected for High-Throughput screening by ELISA for binding to murine PTPRK and an unrelated control protein. PTPRK-specific B cells were lysed and immediately frozen at −80°C until molecular cloning. Variable regions (VH and VL) of each monoclonal antibody from rabbit B cells were then cloned into expression vectors from extracted mRNA as previously described (Seeber et al., 2014). Individual recombinant rabbit antibodies were expressed in Expi293 cells and subsequently purified with protein A. Purified anti-PTPRK antibodies were then subjected to functional activity assays and kinetic screening. Lead clones were selected for large scale antibody production.

Lipid-based transfection of siRNA duplexes

Cells were transfected with siRNA duplexes using lipofectamine RNAiMAX (Thermo Fisher Scientific). For a 6-well plate, 15 μl of 2 μM siRNA duplexes were added to 481 μl of serum/antibiotic-free OptiMEM (Thermo Fisher Scientific) and allowed to settle at RT for 5 min. 4 μl of lipofectamine RNAiMAX was then added, the mixture inverted briefly and incubated at RT for 20 min. Cells were seeded at 1.25–2.5 × 105 cells/ml in a 1 ml volume of complete growth medium, followed by immediate dropwise addition of the siRNA/lipofectamine mixture to give a final siRNA concentration of 20 nM. Cells were returned to the incubator after 30 min at RT. After 24 hr total incubation, media were replaced for complete growth medium. Cells were allowed to recover for 48–72 hr prior to treatment or processing for analysis. All siRNA duplexes where purchased from Dharmacon (Horizon Discovery, UK).

CRISPR/Cas9 genome editing

Oligos for single guide RNAs targeting exons 1 and 2 of PTPRK were cloned into pspCas9.(BB).eGFP as previously described (Ran et al., 2013). MCF10A cells were transfected with plasmids using Lipofectamine LTX with PLUS Reagent as per manufacturer’s instructions (Thermo Fisher Scientific). After 48 hr eGFP positive cells were single-cell sorted using flow cytometry. Clones were expanded and protein levels assessed by Western blot. Targeted regions of the genome were amplified by PCR and sequenced to confirm editing.

Lentivirus production and infection

15 × 106 HEK293T cells were seeded in 12 ml of complete growth medium/15 cm2 dish (two dishes per lentivirus) and incubated for 24 hr at 37°C with 5% CO2. Each 15 cm2 dish was then transfected with either 6 μg of pCW57.GFP.2A. or pLenti.puro expression plasmid encoding the desired construct, 12 μg of the psPAX2 packing plasmid (a gift from Didier Trono; #12260, Addgene) and 3 μg of the pMD2.G envelope plasmid (a gift from Didier Trono; #12259, Addgene) using the GeneJuice transfection reagent (Merck Millipore, UK) as per manufacturer’s instructions. After 24 hr media was then replaced with 16 ml complete growth medium. 48–72 hr post-transfection, culture medium was collected and filtered through a 0.45 μm mixed cellulose esters membrane. Viral particles were pelleted via ultracentrifugation at 100,000 x g for 1.5 hr at 4°C and resuspended in 600 μl of OptiMEM (Thermo Fisher Scientific). Lentivirus was aliquoted and stored at −80°C until required.

For lentiviral infections, 1.6 × 105 cells were seeded per well of a six well plate in 900 μl of growth medium, prior to the drop-wise addition of 100 μl lentivirus. After 30 min at room temperature (RT), cells were returned to the incubator. 72 hr later cells were reseeded in 0.4 μg/ml puromycin (Gibco, Thermo Fisher Scientific) selection medium.

PTPRK extracellular domain screen

PTPRK ECD was expressed in HEK293S cells and purified using standard affinity chromatography procedures. Purified recombinant PTPRK ECD was screened as protein A microbeads complexes, carrying a Cy5-labeled IgG as an inert carrier to allow visualization of any binding partners against the Extracellular Protein Microarray Technology, as described previously (Martinez-Martin et al., 2016; Yeh et al., 2016). This platform (consisting of >1500 purified proteins, representing ≈50% of the single transmembrane-containing receptors in humans), in combination with a query protein multimerization approach for enhanced detection of binding partners, has enabled identification of multiple interactions between extracellular proteins (Martinez-Martin et al., 2016; Yeh et al., 2016), including low affinity interactions that often characterize receptors expressed on the cell surface (Martinez-Martin, 2017; Wright, 2009).

Pervanadate treatment

Two × 106 cells were seeded per 10 cm2 dish and cultured for 6 days with a media change on day 3 and day 5. Cells were stimulated with 6 ml of complete growth medium containing 1 mM fresh sodium pervanadate (made as outlined below) for 30 min at 37°C/5% CO2. Cells were then transferred onto ice and washed twice with ice-cold PBS, prior to the addition of 600 μl of ice-cold lysis buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 10% (v/v) glycerol, 1% (v/v) triton X-100, 1 mM EDTA, 5 mM iodoacetamide, 1 mM sodium orthovanadate, 10 mM NaF, 1X EDTA-free protease inhibitors (Roche, UK)), and incubated on a rocker at 4°C in the dark. Lysates were harvested, followed by the addition of DTT to a final concentration of 10 mM and incubated for 15 min on ice. Lysates were cleared by centrifugation at 14000 x g for 15 min at 4°C and supernatants were transferred into fresh tubes. Pervanadate-treated cell lysates were then snap frozen and stored at −80°C until required.

To generate a 50 mM pervanadate working stock, 5 μl of 3% (w/v) H2O2 (Thermo Fisher Scientific) was diluted in 45 μl of 20 mM HEPES pH 7.3 prior to the addition of 490 μl of 100 mM Na3VO4 (Alfa Aesar, Thermo Fisher Scientific) and 440 μl of H2O, the solution was mixed by gentle inversion and incubated at RT for 5 min. After 5 min, a small amount of catalase (Sigma-Aldrich) was added to the pervanadate solution using a pipette tip and mixed by gentle inversion to quench unreacted H2O2. Freshly made pervanadate solution was used within 5 min to avoid decomposition of the complex.

RT-qPCR

RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, UK) according to the manufacturer’s instructions. cDNA was prepared using the High-Capacity cDNA Reverse Transcription Kit as per manufacturer’s instructions (Applied Biosystems). RT-qPCR was performed using the TaqMan Universal Master Mix II (Applied Biosystems, Thermo Fisher Scientific), 50 ng cDNA and specific Taqman probes for PTPRK, PTPRM, PTPRT, PTPRU and RPL19 Real-time PCR was performed with the 7900HT Fast Real-Time PCR System (Thermo Fisher Scientific). Expression levels were normalized to the reference gene RPL19. Gene specific primers are listed in the Key Resources table.

SDS-PAGE and immunoblotting

SDS PAGE and immunoblotting were carried out as previously described (Fearnley et al., 2015). 25–50 μg of cell lysate was resuspended in an appropriate volume of 5X SDS-PAGE sample buffer (0.25 M Tris-HCl pH 6.8, 10% (w/v) SDS, 20% (v/v) glycerol, 0.1% (w/v) bromophenol blue, 10% (v/v) β-mercaptoethanol) and incubated at 92°C for 5 min. Samples were run on a 8, 10 or 12% (v/v) SDS-polyacrylamide resolving gel with a 5% (v/v) SDS-PAGE stacking gel and subjected to electrophoresis at 120–130 V for ~1–2 hr in 25 mM Tris, 190 mM glycine, 0.1% (w/v) SDS. Proteins were transferred onto 0.2 µm reinforced nitrocellulose membranes (GE Healthcare) at 300 mA for 3–4 hr at 4°C in 25 mM Tris, 190 mM glycine, 20% (v/v) methanol. Membranes were briefly rinsed in TBS-T (20 mM Tris pH 7.6, 137 mM NaCl, 0.1% (v/v) Tween-20) prior to incubation for 20–60 min in 5% (w/v) skimmed milk/TBS-T to block non-specific antibody binding. The blocking solution was removed and membranes rinsed in TBS-T prior to primary antibody incubation (4–5 hr at RT or overnight at 4°C). Membranes were then subjected to 3 × 10 min washes in TBS-T, prior to incubation with HRP-conjugated species-specific anti-IgG antibodies (1–2 hr at RT). Membranes were then subjected to 3 × 10 min washes in TBS-T, prior to being incubated with combined EZ-ECL solution (Geneflow, UK) and imaged using a Bio-Rad ChemiDoc MP imaging system.

Expression, biotinylation (AviTag) and purification of recombinant proteins

Escherichia coli BL21(DE3) Rosetta cells transformed with the relevant expression construct were cultured at 30°C/220 rpm in 1 l of 2XTY medium containing 50 μg/ml carbenicillin and 34 μg/ml chloramphenicol until the OD600 reached 0.6–0.7. Cultures were then transferred to 20°C/220 rpm and allowed to equilibrate, prior to the addition of 1 mM isopropyl-thio-β-D-galactopyranoside (IPTG; Generon, UK) and 200 μM of D-biotin (Sigma-Aldrich). Cells were harvested after 20 hr by centrifugation at 4000 x g for 30 min and bacterial pellets stored at −20°C until required. Prior to lysis, cells were subjected to one round of freeze-thaw. Cells were lysed in purification buffer (50 mM HEPES pH 7.5 for PTP domains (50 mM Tris pH 7.4 for SH2 domain mutants), 500 mM NaCl, 5% (v/v) glycerol and 0.5 mM TCEP), containing EDTA-free protease inhibitor tablets (Roche) using a Constant Systems cell disruptor and the cell extract was clarified via centrifugation at 40000 x g for 30 min at 4°C. The supernatant was removed and incubated with 0.5 ml of Ni-NTA agarose (Qiagen) for 1 hr at 4°C. Ni-NTA Agarose was then pelleted via centrifugation at 500 x g for 5 min at 4°C and packed into a gravity flow column. Ni-NTA agarose was then washed with 10 volumes of purification buffer containing 5 mM imidazole, followed by 20 volumes of purification buffer containing 20 mM imidazole; prior to elution in purification buffer containing 250 mM imidazole. The eluted protein was then subjected to size exclusion chromatography (SEC) using a Superdex 200 16/600 column (GE Healthcare Life Sciences, Thermo Fisher Scientific) for PTP domains or Superdex 75 16/600 column (GE Healthcare Life Sciences, Thermo Fisher Scientific) for SH2 mutant domains. Columns were equilibrated in SEC buffer (50 mM HEPES pH 7.5 (50 mM Tris pH 7.4 for SH2 domains), 150 mM NaCl, 5% (v/v) glycerol, 5 mM DTT). Protein was concentrated to 2–10 mg/ml using an Ultracel-3K, Ultracel-10 K or Ultracel-30 K regenerated cellulose centrifugal filter (Merck Millipore), prior to snap-freezing and storage at −80°C until required. The purified protein was assessed by SDS-PAGE and staining with InstantBlue (Expedeon, UK).

Confirmation of AviTag biotinylation via streptavidin gel shift assay

Biotinylated recombinant proteins (2–10 μg) were solubilized in 4 μl of 5X SDS-PAGE sample buffer and incubated at 95°C for 5 min. Samples were then cooled to RT and allowed to equilibrate for 5 min. 24 μl of 2 mg/ml streptavidin/PBS (approx. 5-fold molar excess) was then added and the mixture was incubated at RT for 5 min. Samples were then run on a NuPAGE 4–12% Bis-Tris gel (Thermo Fisher Scientific) in NuPAGE MES (2-ethanesulfonic acid) gel running buffer (Thermo Fisher Scientific) at 190 V for 30 min. Protein only and streptavidin only controls should be included. Proteins were then visualized via staining with InstantBlue (Expedeon) for 1 hr at RT. Gels were imaged using a Bio-Rad ChemiDoc MP imaging system and the percentage of biotinylated protein determined via 2D-densitometry using Fiji (Schindelin et al., 2012).

Recombinant protein pull downs

25–50 μg (tandem or single domain, respectively) of biotinylated His.TEV.Avi.PTPx domains were conjugated to 167 μl of pre-washed streptavidin-coated magnetic beads suspension (4 mg/ml; New England Biolabs) in 500 μl of ice-cold size exclusion buffer (50 mM HEPES pH 7.5 (50 mM Tris pH 7.4 for SH2 domains), 150 mM NaCl, 5% (v/v) glycerol, 5 mM DTT) at 4°C for 1–2 hr on a rotator. A beads-only control was treated identically. Samples were briefly spun, transferred onto a magnetic stand and washed 3 times with 1 ml of ice-cold size exclusion buffer, followed by two washes with 1 ml of ice-cold 150 mM NaCl wash buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 10% (v/v) glycerol, 1% (v/v) triton X-100, 1 mM EDTA pH 8.0). Conjugated PTP domains were then blocked in 1 ml of ice-cold 5% (w/v) BSA in 150 mM NaCl wash buffer containing 1x EDTA-free protease inhibitors (Roche) at 4°C for 1 hr on a rotator. Simultaneously, freshly thawed pervanadate-treated cell lysate was then pre-cleared with streptavidin-coated magnetic beads (167 μl of bead suspension (4 mg/ml) per ml of lysate) at 4°C for 1 hr on a rotator. Blocked conjugated PTPx domains were then briefly spun, transferred onto a magnetic stand and washed twice with 1 ml of ice-cold 150 mM NaCl wash buffer; prior to incubation with 1 ml of 1 mg/ml pre-cleared pervandate-treated lysate at 4°C on for 1.5 hr on a rotator. In a cold room, beads were pulled to a magnet and supernatant removed. Beads were then washed twice in 1 ml ice-cold 150 mM NaCl wash buffer including a brief spin and separation by magnet. Beads were then washed once with 1 ml ice-cold 150 mM NaCl wash buffer without resuspension and washed twice more in 1 ml ice-cold 150 mM NaCl wash buffer with resuspension. Next beads were washed once without resuspension and twice with resuspension in 1 ml ice-cold 500 mM NaCl wash buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 10% (v/v) glycerol, 1% (v/v) triton X-100, 1 mM EDTA pH 8.0). Finally, beads were washed once without resuspension and once with resuspension in 1 ml ice-cold TBS (20 mM Tris pH 7.6, 137 mM NaCl). For immunoblot analysis, beads were resuspended in 20 μl of 18% (v/v) formamide,1 mM EDTA pH 8.0 made up in TBS, incubated at 95°C for 5 min, followed by addition of 30 μl of 5x SDS-PAGE sample buffer containing 2 mM biotin and incubated at 95°C for 10 min. After a brief spin, beads were separated by magnet and supernatants subjected to SDS-PAGE. For analysis by mass spectrometry, beads were subject to two further washes without resuspension and one further wash with resuspension in 1 ml ice-cold 50 mM ammonium bicarbonate pH 8.0, followed by on-bead tryptic digest.

On-bead tryptic digest

Streptavidin beads for tryptic digest were resuspended in 95 μl of 50 mM ammonium bicarbonate pH 8.0, prior to the addition of 5 μl of 100 mM DTT (5 mM final DTT concentration), and incubation at 56°C for 30 min. 10 μl of 154 mM iodoacetamide (IAA) was then added (14 mM final IAA concentration) and samples incubated in the dark at RT for 20 min. Unreacted IAA was then quenched by the addition of 7 μl of 100 mM DTT (10 mM final DTT concentration), and incubation at RT for 15 min. Next, 31.5 μl of 50 mM ammonium bicarbonate pH 8.0 and 1.5 μl of LysC (0.005 AU/μl; Wako) was added to each sample, followed by incubation at RT for 3 hr with shaking. 150 μl of 7.7 ng/μl trypsin (Thermo Fisher Scientific) in 50 mM ammonium bicarbonate pH 8.0) was added to each sample (3.84 ng/μl final trypsin concentration) and incubate at 37°C overnight with shaking. An additional 150 μl of 7.7 ng/μl trypsin was then added to each sample (5.1 ng/μl final trypsin concentration), followed by incubation at 37°C for 2 hr with shaking. Samples were briefly spun and placed onto a magnetic stand, supernatant was then transferred into a low protein-binding tube (Eppendorf, Thermo Fisher Scientific). Beads were then washed twice with 150 μl of proteomics grade water (Thermo Fisher Scientific) and resulting supernatants added to the first supernatant. Samples were then centrifuged at 18400 x g for 10 min at 4°C and supernatant transferred into a new low protein-binding tube. Samples were then adjusted to 1% (v/v) TFA, prior to centrifugation at 21000 x g for 10 min at 4°C and supernatants transferred into a new low protein-binding tube. Each tryptic digest was desalted using a 1cc/50 mg Sep-Pak C18 cartridge (Waters). All buffers were made using proteomics grade water. Sep-Paks were equilibrated via washing with twice with 1 ml 100% (v/v) acetonitrile (AcN; VWR), twice with 1 ml 50% (v/v) AcN/0.1% (v/v) TFA and twice with 1 ml 0.1% (v/v) TFA. Samples were then slowly loaded onto each Sep-Pak; flow-through was reapplied once. Sep-Paks were then washed three times with 1 ml 0.1% (v/v) TFA. Peptides were then eluted into a new low protein-binding tube by addition of two 350 μl volumes of 50% (v/v) AcN/0.1% (v/v) TFA. Peptide samples were then dried down using a vacuum centrifuge (Concentrator 5301, Eppendorf) at 30–45°C. Peptide pellets were then stored at −20°C until further processing.

Mass spectrometry acquisition and data analysis for pull downs

LC-MS/MS data were acquired on either a Q Exactive (Thermo Fisher Scientific) or a Q Exactive Plus (Thermo Fisher Scientific) each coupled, via an EASYspray source, to an RSLC3000 nanoUHPLC. Peptides were loaded onto a 100 µm ID x 2 cm Acclaim PepMap nanoViper precolumn (Thermo Fisher Scientific) and resolved using a 75 µm ID x 50 cm, 2 µm particle PepMap RSLC C18 EASYspray column at 40°C. NanoUHPLCs were operated with solvent A (0.1% formic acid) and solvent B (80% MeCN, 0.1% formic acid). Peptides were resolved on the Q Exactive by a gradient rising from 3% to 40% B by 60 mins and on the Q Exactive Plus by a gradient ring from 10% to 40% B by 57 min. MS spectra on the Q Exactive were acquired between m/z 400 to 1400 and between m/z 400 to 1500 on the Q Exactive Plus. Both operated MS/MS triggered in a top 10 DDA fashion.

Raw files were processed on MaxQuant v.1.5.2.8 or 1.5.8.3. using default settings. Quantification was carried out using Perseus ver. 1.5.8.5 (Tyanova et al., 2016). For label-free quantification (LFQ), LFQ intensities from MaxQuant were log2(x) transformed prior to filtering out proteins branded as identified only by site, reverse or potential contaminants. Proteins were then further filtered out based on the minimum number of valid values in one group, to be stringent we required a minimum of three (MCF10A experiments) or two (Hs27 experiments) valid values. Missing values were then imputed from the normal distribution and statistical significance was calculated via a two-sample, two-sided t test performed with truncation by a permutation-based FDR (threshold value 0.05). High confidence interactors were defined as >2 fold enrichment (over beads only), significant (p>0.05) and a CRAPome score ≤137 (Mellacheruvu et al., 2013).

pNPP phosphatase activity assay

All buffers were made in phosphate-free H2O (Thermo Fisher Scientific). Recombinant phosphatase was added to a 96-well plate in a total volume of 50 μl reaction buffer (50 mM HEPES pH 7.4, 150 mM NaCl, 5% (v/v) glycerol, 5 mM DTT). 50 μl of reaction buffer containing 20 mM pNPP (New England Biolabs) was then added and the plate was incubated at RT for 3–15 min. Reactions were stopped by the addition of 50 μl 0.58 M NaOH (0.193 final concentration) and the absorbance read at 405 nm using a 96-well plate reader (SpectraMax M5, Molecular Devices, UK).

BIOMOL green phosphatase activity assay

All buffers were made in phosphate-free water (Thermo Fisher Scientific). In a 96-well plate, 30 μl of reaction buffer containing 100 μM each of DADE-pTyr-LIPQQG-Acid phosphopeptide and END-pTyr-INASL-Acid phosphopeptides (Cambridge Research Biochemicals) was incubated at 30°C for 3 min, prior to the addition of recombinant phosphatase in a total volume of 20 μl reaction buffer. The assay was then incubated at RT for 2.5–3.5 min. Reaction was stopped by the addition of 100 μl of BIOMOL Green reagent (ENZO, UK), followed by incubation at RT for 15–30 min. The absorbance was then read at 620 nm using a 96-well plate reader (SpectraMax M5, Molecular Devices). Enzyme activity was compared against a standard curve from serial dilutions of a phosphate standard (ENZO).

Quantitative tyrosine phosphoproteomics and total proteomics

2 × 106 WT or PTPRK-KO SILAC labeled MCF10A cells were seeded into three 10 cm2 dishes in heavy (WT) or light (PTPRK-KO) SILAC medium for each experiment. Cells were cultured for 7 days with a media change on days 2 (10 ml), 4 (12 ml), 5 (12 ml) and 6 (12 ml). On day 7, cells were placed on ice, washed twice with ice-cold PBS and lysed in 150 μl of 6M guanidine (Thermo Fisher Scientific) in 50 mM EPPS pH 8.5 (Alfa Aesar) with 1X EDTA-free protease inhibitor cocktail (Roche) and 1X phosphatase inhibitor cocktail (Roche). Samples were transferred into Diagenode sonication tubes (Diagenode, UK) on ice, vortexed at max speed for 30 s and sonicated at 4°C on high power for 5 × 30 s pulses using a water bath sonicator (Bioruptor, Diagenode). Samples were cleared twice by centrifugation at 13000 x g for 10 min at 4°C with supernatants transferred to new low protein-binding tubes (Eppendorf). Protein concentration was then determined by BCA assay and equal amounts of heavy and light labeled protein lysates were transferred into 5 ml low protein-binding tubes (Eppendorf) to give a maximum combined volume of 600 μl. A total of 10 mg of protein from heavy and light lysates was processed per replicate. Proteins were reduced by addition of 30 μl DTT/200 mM EPPS pH 8.5 (5 mM final DTT concentration), vortexed and incubated at RT for 20 min. Proteins were then alkylated by addition of 16.8 μl of 500 mM IAA/200 mM EPPS pH 8.5 (14 mM final IAA concentration), vortexed and incubated at RT for 20 min in the dark. Unreacted IAA was quenched via the addition of 30 μl of freshly thawed 100 mM DTT/200 mM EPPS pH 8.5 (8.9 mM final DTT concentration), prior to vortexing and incubation at RT for 15 min. Samples were diluted to a final concentration of 1.5 M guanidine by addition of 1.8 ml 200 mM EPPS pH 8.5. Next, 0.06 AU of LysC (Wako) was added to each sample, prior to vortexing and incubation at RT for 3 hr with shaking. Samples were split in half and transferred to two new 5 ml low protein-binding tubes. Samples were diluted to a final concentration of 0.5 M Guanidine by adding 2.48 ml 200 mM EPPS pH 8.5. 100 μl of 124 ng/μl Trypsin (Thermo Fisher Scientific)/EPPS pH 8.5 was then added to each sample, prior to vortexing and incubation at 37°C overnight with shaking. An additional 100 μl of 124 ng/μl Trypsin/EPPS pH 8.5 was then added, prior to vortexing and incubation at 37°C for 2 hr with shaking. Tryptic digests were then acidified via the addition of 39.8 μl TFA (Thermo Fisher Scientific) or 1% (v/v) TFA final concentration. Samples were then split into two new 2 ml low protein-binding tubes (Thermo Fisher Scientific), prior to centrifugation at 21000 x g for 10 min. Supernatants were transferred to a new 2 ml low protein-binding tubes, prior to being snap-frozen and stored at −80°C or desalted. Tryptic digests were desalted using 1cc/50 mg Sep-Pak Vac tC18 cartridges (Waters, UK); 20 mg/~40 ml of tryptic digest was split across four 1cc/50 mg Sep-Pak Vac tC18 cartridges. Sep-Paks were equilibrate, washed and loaded as described above. Peptides were eluted in a stepwise manner into new 1.5 ml low protein -binding tubes. Fraction 1: 350 μl 12.5% (v/v) AcN/0.1% (v/v) TFA, Fraction 2: 350 μl 25% (v/v) AcN/0.1% (v/v) TFA, Fraction 3: 350 μl 37.5% (v/v) AcN/0.1% (v/v) TFA, Fraction 4: 350 μl 50% (v/v) AcN/0.1% (v/v) TFA. Corresponding fractions were then pooled and 10% (v/v) removed for total proteome analysis. Peptides were then dried down using a vacuum centrifuge (Concentrator 5301, Eppendorf) at 45°C and stored at −20°C until further processing.

For phospho-tyrosine enrichment, peptide fractions were resuspended in 400 μl of ice-cold IAP buffer (50 mM Tris-HCL pH 7.4, 10 mM Na2HPO4 (Acros Organics), 100 mM NaCl) and incubated for 10 min on ice. Added to each fraction was 10 μl of rabbit anti-pY-1000 antibody (Cell Signal Technologies, New England Biolabs) pre-conjugated to 5 μl of protein G agarose bead suspension (Merck Millipore) and 2.4 μg each of biotinylated Src and Grb2 SH2 mutant domains, pre-conjugated to 5 μl of streptavidin agarose bead suspension (Thermo Fisher Scientific) and ice-cold IAP buffer up to 1 ml. Samples were then incubated at 4°C for 16–24 hr on a rotator. Beads were pelleted via at 14000 x g for 30 s and washed three times with 1 ml ice-cold IAP buffer followed by two washes with 1 ml ice-cold proteomics grade water. Peptides from each fraction were eluted in 125 μl of 0.15% (v/v) TFA at RT for 15 min; beads were pelleted and the supernatant transferred to a new 1.5 ml low protein binding tube (Eppendorf). This step was repeated for a total of three elutions and supernatants combined. Eluted peptides were then desalted using graphite spin columns (Thermo Fisher Scientific), according to manufacturer’s instructions, using two columns per fraction, and dried down using a vacuum centrifuge at 45°C. For further enrichment of phospho-peptides using TiO2, peptide fractions were resuspended in 100 μl 2% (v/v) TFA and incubated at RT for 10 min. Each fraction was then split and processed on two Titansphere Phos-TiO Tips (200 μl/3 mg; GL Sciences Inc) as per manufacturer’s instructions. Peptides were eluted in 50 μl of 5% (w/v) NH4OH (35% w/v; Acros Organics, Thermo Fisher Scientific), followed by 50 μl of 60% (v/v) AcN. Peptide samples were then dried down using a vacuum centrifuge at 45°C, prior to storage at −20°C or −80°C before analysis by mass spectrometry.

Mass spectrometry acquisition and data analysis for quantitative tyrosine phosphoproteomics and total proteomics

Samples were resuspended in 20 μL sample solution (3% MeCN, 0.1% trifluroacetic acid). LC-MS/MS data acquisition was performed on a Q Exactive Plus and an Orbitrap Fusion Lumos (Thermo Fisher Scientific) with both instruments configured to RSLC3000 nanoUHPLCs. Both the Q Exactive Plus and the Fusion Lumos were operated with an EASYspray source using a 50 cm PepMap EASYspray emitter at 40°C. The Fusion Lumos was also operated using a 75 cm Acclaim PepMap column at 55°C with SilicaTip coated emitters (New Objective, USA). All nanoHPLCs were operated with solvent A (0.1% formic acid) and solvent B (80% MeCN, 0.1% formic acid).

Total peptides were resolved using four different gradients. Gradient 1 (for sample fraction 1) rose from 3% to 15% solvent B by 125 min and 40% B by 175 min. Gradient 2 (for sample fraction 2) rose from 3% to 25% B by 125 min and 40% B by 175 min. Gradient 3 (for sample fraction 3) rose from 3% to 40% B by 175 min and gradient 4 (for sample fraction 4) rose from 12% to 58% B by 175 min.

Phosphopeptides were resolved using four different gradients. Gradient 1 (for sample fraction 1) rose from 3% to 15% solvent B by 70 min and 40% B by 95 min. Gradient 2 (for sample fraction 2) rose from 3% to 25% B by 80 min and 40% B by 95 min. Gradient 3 (for sample fraction 3) rose from 10% to 40% B by 95 min and gradient 4 (for sample fraction 4) rose from 15% to 50% B by 95 min. MS/MS data on the Q Exactive Plus were acquired in a Top10 DDA fashion and on the Fusion Lumos MS/MS data were acquired in the ion trap using a 3 s cycle.

Data were processed using MaxQuant v.1.6.2.3 with a Uniprot Homo sapiens database (downloaded 28/1/2018). Variable modifications were set as oxidation (M), acetylation (protein N-terminus) and phospho (STY) with ‘re-quantify’ and ‘match between runs’ enabled. Peptide and protein FDR were set to 0.01. Quantification was carried out using Perseus ver. 1.5.8.5 (Tyanova et al., 2016). Normalized H/L ratios from MaxQuant were log2(x) transformed prior to filtering out proteins labeled as identified only by site or reverse. Proteins were then further filtered out based on the minimum number of valid values; a minimum of two valid values were required for high confidence analysis. Missing values were then imputed from the normal distribution and log2(x) transformed normalized H/L SILAC ratios were inverted, prior to averaging. Statistical significance was calculated via a one-sample, two-sided t test performed with truncation by a Benjamini Hochberg FDR (threshold value 0.05).

Identification of cellular interactors using BioID

4 × 106 WT MCF10A cells stably transduced with pCW57.tGFP, pCW57.tGFP.P2A.PTPRK.C1089S-BirA*-FLAG or pCW57.tGFP.P2A.PTPRK.1–785.BirA*-FLAG were seeded into 10 cm2 dishes (three per condition). 24 hr after seeding, media was changed and doxycycline was added at 500 ng/ml for PTPRK.C1089S-BirA*-FLAG and tGFP, and 150 ng/ml for PTPRK.1–785-BirA*-FLAG. On the fourth day, doxycycline containing media was replaced and supplemented with 50 μM biotin (Sigma-Aldrich). After 24 hr, cells were lysed in 600 μl RIPA buffer (50 mM Tris–HCl pH 7.5, 150 mM NaCl, 1% (v/v) NP-40, 0.5% (w/v) sodium deoxycholate, 1 mM EDTA, 0.2% (w/v) SDS) and complete protease inhibitor cocktail (Roche). Cell lysates were then sonicated and clarified at 16500 x g for 10 min at 4°C. Equal amounts (3–4 mg) of lysate were transferred into 1.5 ml tubes which contained 50 μl of streptavidin agarose bead suspension (Thermo Fisher Scientific) that had previously been washed in RIPA buffer. Samples were then made up to 1 ml total volume in RIPA buffer and incubated at 4°C on a rotator overnight. Beads were pelleted at 14000 x g for 30 s at 4°C, supernatant removed and beads washed once with 1 ml 2% (w/v) SDS in PBS, followed by two washes with 1 ml 50 mM NaCl, 1% (v/v) NP-40, 50 mM Tris pH 7.5% and 0.2% (w/v) SDS including 8 min incubations on a rotator at RT. Proteins were eluted by incubation at 92°C in SDS sample buffer supplemented with 3 mM biotin for 10 min, prior to immunoblot analysis.

In lysate dephosphorylation assay

All steps were performed on ice unless indicated. Each recombinant phosphatase domain was added to a total volume of 342 μl ice-cold 150 mM NaCl wash buffer to which 50 μl (200 μg) of freshly thawed pervanadate-treated cell lysate was added. Samples were mixed by gentle inversion and reactions were then incubated for 1.5 hr at 4°C on a rotator. 8 μl of 20% (w/v) SDS was then added (0.4% (w/v) final SDS concentration), samples were vortexed and incubated for 5–10 min. Samples were then diluted with 400 μl ice-cold 150 mM NaCl wash buffer to 0.2% (w/v) SDS final concentration and vortexed; prior to the addition of 5 μl of rabbit-anti-phospho-tyrosine antibody (Cell Signaling Technology). Samples were then incubated for 2–4 hr at 4°C on a rotator. 40 μl of washed protein G agarose bead suspension (Merck Millipore) was then added, prior to incubation overnight at 4°C on a rotator. Beads were pelleted at 15000 x g for 30 s at 4°C and washed five times in 1 ml of ice-cold 150 mM NaCl wash buffer. After the final wash, beads were transferred to RT and resuspended in SDS-PAGE sample buffer and incubated at 92°C for 10 min. Beads were pelleted at 15000 x g for 30 s and the supernatant transferred into a new microfuge tube. Samples were stored at −20°C prior to SDS-PAGE and immunoblot analysis.

Protein structure presentation and homology modeling

All manipulations and homology modeling based on existing structures were performed using University of California San Francisco (UCSF) Chimera (Pettersen et al., 2004).

Immunostaining MCF10A monolayers

5 × 105 cells were seeded in 3 ml of complete growth medium on 18 mm x 18 mm,1.5 mm thick high-performance coverslips (Zeiss, UK). Cells were cultured for 6 days, with a media change on day 3, and then every day thereafter. On day 6, media was removed and cells fixed in 500 μl of methanol-free 4% (w/v) para-formaldehyde (PFA; Thermo Fisher Scientific) in PBS for 10 min at RT. Coverslips were then rinsed with 5 × 500 μl of PBS, followed by permeabilization in 500 μl of 0.5% (v/v) triton X-100, 3% (w/v) BSA in PBS for 2 min at room temperature and blocking in 1 ml of 0.2% (v/v) triton X-100, 3% (w/v) BSA in PBS for 1 hr at RT. Coverslips were then incubated with primary antibody (1:100 dilution) for 1–5 hr at RT. followed by five 500 μl 5 min washes with 0.2% (v/v) triton X-100, 3% (w/v) BSA in PBS. Coverslips were then incubated with species-specific fluorophore- conjugated anti-IgG antibodies (1:250 dilution) containing Hoechst 33342 (1:2000; Thermo Fisher Scientific) with or without BODIPY 558/568 phalloidin (1:250; Thermo Fisher Scientific), for 45–60 min at RT in the dark. Coverslips were then rinsed twice with 500 μl 0.2% (v/v) triton X-100, 3% (w/v) BSA in PBS, followed by three 500 μl washes (5 min) with PBS. Coverslips were then mounted onto 1.0 mm thick slides using ProLong Gold antifade (Thermo Fisher Scientific). Slides were imaged using either a LSM880 confocal, LSM710 confocal, Elyra PS1 Super resolution or an AxioImager Z2 microscope (Zeiss).

MCF10A spheroid cultures and immunostaining

MCF10As were cultured as spheroids following the previously described ‘3D on-top’ method (Lee et al., 2007). 96-well plates were chilled for 30 min in the fridge before use. 15 μl Matrigel (Corning, Thermo Fisher Scientific), was spread evenly on the bottom of each well and allowed to set at 37°C for 20 min. 5 × 103 MCF10A cells per well were resuspended in MCF10A growth media and layered on top of the matrix and incubated for 20 min. 30 μl MCF10A growth media containing 10% (v/v) Matrigel was then added on top of the cells. Media was replaced with 30 μl complete growth media and 2% (v/v) Matrigel every 2–3 days for 7 days and then switched to EGF-free MCF10A growth media and 2% (v/v) Matrigel for 7 days. Acini were imaged at 10x magnification on day 14, using the EVOS FL Cell Imaging System (Thermo Fisher Scientific).

Spheroids were extracted from Matrigel as previously described (Lee et al., 2007). Media was aspirated and wells washed twice with PBS. Spheroids were extracted using 5 mM EDTA in PBS and gentle shaking for 30 min. Spheroids were then briefly centrifuged at 115 x g and the majority of supernatant aspirated. The remaining supernatant was used to resuspend the spheroids prior to transferring them onto a glass slide. Spheroids were fixed in 4% (v/v) paraformaldehyde (Thermo Fisher Scientific) for 20 min at RT and then permeabilized with 0.5% (v/v) Triton X-100 for 10 min at 4°C. The fixed spheroids were then washed three times in 100 mM glycine in PBS with 10 min per wash. Next, the spheroids were blocked in IF buffer (0.1% (w/v) BSA; 0.2% (v/v) Triton X-100; 0.05% (v/v) Tween-20) with 10% (v/v) normal serum block (BioLegend, USA) for 60 min at RT. Primary antibody was incubated overnight at 4°C then washed three times with IF buffer. Secondary antibody was incubated for 45 min at RT. The spheroids were then washed once with IF buffer for 20 min, followed by two subsequent washes with PBS for 10 min each. They were then mounted with Prolong Gold Antifade Mounting medium (Thermo Fisher Scientific) and imaged using an LSM880 confocal or an AxioImager Z2 microscope (Zeiss).

Quantification of confocal microscopy images

For immunostained cell monolayers, five random fields were imaged per condition and the results averaged. Image analysis was carried out using Fiji. The Pearson correlation coefficient for two images was determined using the Coloc2 plugin; whilst the fluorescence intensity of an image was analyzed using a custom macro: run(‘Auto Threshold’, ‘method = Default ignore_black white’); run(‘Set Measurements...‘, ‘integrated limit display redirect = None decimal = 3’); run(‘Measure’).

For spheroids, aberrant spheroids were quantified using bright field images of 6 independent wells of WT and PTPRK KO MCF10A spheroids. three non-overlapping images from each well were manually counted for aberrant spheroids. Spheroid diameter was calculated using the circle measurement tool in Zen Pro (Zeiss). A circle was traced around individual spheroids in whole slide images for WT and PTPRK KO MCF10A spheroids using the Hoechst channel.

BrdU incorporation ELISA

In a 96-well plate, 1 × 104 MCF10A cells per well were seeded in 90 μl of complete growth medium and cultured for 2 days. A final concentration of 10 μM bromodeoxyuridine (BrdU) was added to each well and left to incorporate for 2 hr. A BrdU-based cell proliferation ELISA was then performed according to manufacturer’s instructions (Roche, Germany). Absorbance was measured at 370 nm (reference wavelength 492 nm) using a 96-well plate reader (SpectraMax M5, Molecular Devices).

Trans-epithelial electrical resistance (TEER)

5 × 105 cells were seeded in 500 μl of complete growth medium onto the apical side of a 0.4 μm pore size Transwell filter (Corning) inserted into a 24-well companion plate containing (Corning) 500 μl of complete growth medium. Cells were cultured for 6–7 days to allow formation of a complete monolayer, with a media change day three and then every day thereafter. Growth medium was replaced 24 hr prior to TEER assessment; 5–10 readings were taken using a Millicell ERS-2 Volt/Ohm meter (Merck Millipore) and a mean was calculated. TEER value was calculated as follows: (Sample average TEER measurement (Ω) – Blank average TEER measurement (Ω)) x Trans-well surface area (0.3 cm2).

Fluorescein isothiocyanate (FITC)-dextran cell permeability assay

Cells were seeded on the apical side of transwell filters as described for TEER experiments. Growth medium was replaced 24 hr prior the addition of 250 kDa-FITC-dextran (3 mg/ml final concentration; Sigma-Aldrich) to the apical side of the insert; cells were then incubated for 24 hr. After 24 hr inserts were removed and the basal media was mixed by gentle pipetting. Per condition, 4 × 100 μl samples were transfer into a 96-well plate and the fluorescence intensity was measured using a 96-well plate fluorimeter (SpectraMax M5, Molecular Devices) at excitation 494 nm and emission at 515 nm.

Accession codes

The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository (Vizcaíno et al., 2016) with the dataset identifier PXD013055.

References

  1. 1
  2. 2
  3. 3
  4. 4
  5. 5
  6. 6
  7. 7
  8. 8
  9. 9
  10. 10
  11. 11
  12. 12
  13. 13
  14. 14
  15. 15
    Regulation, substrates and functions of src
    1. MT Brown
    2. JA Cooper
    (1996)
    Biochimica Et Biophysica Acta (BBA) - Reviews on Cancer 1287:121–149.
    https://doi.org/10.1016/0304-419X(96)00003-0
  16. 16
  17. 17
  18. 18
  19. 19
  20. 20
  21. 21
  22. 22
  23. 23
  24. 24
  25. 25
  26. 26
  27. 27
  28. 28
  29. 29
  30. 30
    Detection and Quantification of Vascular Endothelial Growth Factor Receptor Tyrosine Kinases in Primary Human Endothelial Cells
    1. GW Fearnley
    2. SB Wheatcroft
    3. S Ponnambalam
    (2015)
    In: L Fiedler, editors. In VEGF Signaling: Methods and Protocols. New York: Springer. pp. 49–65.
  31. 31
  32. 32
  33. 33
  34. 34
    Cell-cell adhesion mediated by a receptor-like protein tyrosine phosphatase
    1. MF Gebbink
    2. GC Zondag
    3. RW Wubbolts
    4. RL Beijersbergen
    5. I van Etten
    6. WH Moolenaar
    (1993)
    The Journal of Biological Chemistry 268:16101–16104.
  35. 35
  36. 36
  37. 37
  38. 38
  39. 39
  40. 40
  41. 41
  42. 42
  43. 43
  44. 44
  45. 45
  46. 46
  47. 47
  48. 48
  49. 49
  50. 50
  51. 51
  52. 52
  53. 53
  54. 54
  55. 55
  56. 56
  57. 57
  58. 58
  59. 59
  60. 60
  61. 61
  62. 62
  63. 63
  64. 64
  65. 65
  66. 66
  67. 67
  68. 68
  69. 69
  70. 70
  71. 71
  72. 72
  73. 73
  74. 74
  75. 75
  76. 76
  77. 77
  78. 78
  79. 79
  80. 80
  81. 81
  82. 82
  83. 83
  84. 84
  85. 85
  86. 86
  87. 87
  88. 88
  89. 89
  90. 90
  91. 91
  92. 92
  93. 93
  94. 94

Decision letter

  1. Tony Hunter
    Reviewing Editor; Salk Institute for Biological Studies, United States
  2. Jonathan A Cooper
    Senior Editor; Fred Hutchinson Cancer Research Center, United States
  3. Tony Hunter
    Reviewer; Salk Institute for Biological Studies, United States
  4. Alpha Yap
    Reviewer; University of Queensland, Australia
  5. Michel Tremblay
    Reviewer; McGill University

In the interests of transparency, eLife includes the editorial decision letter and accompanying author responses. A lightly edited version of the letter sent to the authors after peer review is shown, indicating the most substantive concerns; minor comments are not usually included.

[Editors’ note: a previous version of this study was rejected before peer review, but the authors submitted for reconsideration. The first decision letter before peer review is shown below.]

Thank you for choosing to send your work entitled "Systematic substrate identification indicates a role for the receptor tyrosine phosphatase PTPRK in epithelial cell-cell adhesion" for consideration at eLife. Your initial submission has been assessed by a Senior Editor in consultation with a member of the Board of Reviewing Editors. Although the work is of interest, we are not convinced that the findings presented have the potential significance that we require for publication in eLife. However, we would encourage you to resubmit if you can provide an additional piece of data, as described below.

The paper presents a detailed study of a receptor type protein tyrosine phosphatase, PTPRK, which was suspected to form homophilic interactions and respond to cell contact. PTPRK gene fusions are found in some cancers, and expression is induced by TGFb. The authors used quantitative proteomics with a "substrate trapping" mutant, expressed in bacteria, to pull out and identify potential substrates. Specificity was confirmed by Westerns, using the related PTP, PTPRM, as a specificity control. They then made PTPRK KO MCF10A cells and identified pY sites undergoing increased phosphorylation. There was an increase in several cell-cell junction proteins, including ones identified as binding to the substrate trapping mutant. BioID confirmed interactions between PTPRK and the proposed substrates in confluent MCF10A cells. Substrates were then tested for dephosphorylation by PTPRK in vitro. MCF10A cell lysates were incubated with recombinant PTPRK. p120Ctn and Afadin (AF6) were dephosphorylated and the sites identified. Three other substrates were identified with high confidence and several others as good candidates. They demonstrate the importance of the pseudophosphatase domain, as well as the phosphatase domain, in substrate recognition. Finally, PTPRK KO alters junction status in MCF10A cells, and alters growth and 3D acini formation. The data showing discrete colocalization of PTPRK and junctional proteins are also nice.

What sets this paper apart is that many different proteomics approaches were used to identify proteins that appear to be substrates in vivo. The use of MCF10A knockouts and reconstituting with wildtype PTPRK or the phosphatase dead mutant is a real plus. However, what is missing is direct evidence of the importance of any of the identified PTPRK sites in cell-cell junction proteins in the integrity of cell-cell junctions, or whether D1 PTP activity is required to reverse the observed MCF10A cell phenotypes. Reviewers are bound to ask and it would not be productive send it for review only to have it rejected because the significance of the phosphatase activity isn't clear. We would not expect the relevance of individual substrates or pY sites to be established, but it is important to test whether the PTP activity is required.

Less major points include whether the in vitro interactions with the WT PTPRK ICD or the substrate trapping mutant D1 domains were in fact dependent on pTyr residues, i.e. they did not treat the lysate with recombinant PTP prior to doing the pulldowns. A significant number of proteins bound selectively to the WT PTPRK ICD vs beads, but since the D1 catalytic domain was active, presumably these interactions were not pTyr dependent. This raises the general issue of the extent to which PTPRK interacting proteins associate directly via a target pTyr as opposed to secondary interactions, for instance those with the inactive D2 domain. In this regard, their model that D2 might recruit targets for D1 does not make much sense, unless the protein has two pTyr residues, since a pTyr bound to D2 would be protected from dephosphorylation by D1.

Another issue that is not discussed is whether there is a primary sequence preference for sites dephosphorylated by D1 – they have a number of identified sites but there is no sequence comparison.

[Editors’ note: what now follows is the decision letter after the authors submitted for in depth peer review.]

Thank you for submitting your article "The homophilic receptor PTPRK selectively dephosphorylates multiple junctional regulators to promote cell-cell adhesion" for consideration by eLife. Your article has been reviewed by three peer reviewers, including Tony Hunter as the Reviewing Editor and Reviewer #1, and the evaluation has been overseen by Jonathan Cooper as the Senior Editor. The following individuals involved in review of your submission have agreed to reveal their identity: Αlpha Yap (Reviewer #2); Michel Tremblay (Reviewer #3).

The reviewers have discussed the reviews with one another and the Reviewing Editor has drafted this decision to help you prepare a revised submission.

As you will see, two out of the three reviewers would have liked to see evidence that dephosphorylation of one or more of the PTPRK target proteins you identified is in fact important for regulating junctional integrity, but after discussion, we have decided that your new data showing that PTPRK activity is important for establishment of cell-cell junctions will suffice for this first paper. No further experiments are required, but please address the other points that the reviewers raised concerning the revised version of your paper. Thank you for submitting your paper to eLife.

Reviewer #1:

Given the reported connections between loss of function mutations in the PTPRK receptor phosphatase and cancer progression, which implicate it as a tumor suppressor, the authors' efforts to define specific substrates for PTPRK are important. They have used a wide variety of different approaches to achieve this goal, including recombinant substrate trapping protein pull down AP-MS proteomics combined with BirA tagging BioID detection of proteins in the vicinity of PTPRK in cells, and pTyr proteomics with PTPRK knockout MCF10A cells, reconstituted with WT or a catalytically-dead PTPRK mutant, to identify pTyr sites that changed when PTPRK activity was increased or decreased. These studies led to the identification of Afadin, PARD3, p120 catenin and PKP3 and PKP4, proteins that are all functionally linked to cell-cell junctions, as candidate specific substrates for PTPRK. By in vitro dephosphorylation of cell lysate proteins with recombinant PTPRK-ICD, using recombinant PTPRM-ICD as a specificity control, they identified two pTyr sites in p120 catenin that could be directly dephosphorylated by PTPRK. Finally, using the MCF10A PTPRK knockout cells, they showed that these cells exhibit defects in E-cadherin junctional contacts, and that re-expression of WT, but not catalytically-dead PTPRK, was able to partially restore the presence of E-cadherin at cell-cell junctions.

The identification of a small set of specific pTyr substrates for PTPRK is an advance in our understanding of this receptor PTP. The known junctional functions of the specific substrates clearly points towards a role for PTPRK in controlling cell-cell junctions, and the confirmatory evidence that PTPRK D1 catalytic activity is required for formation of proper cell-cell junctions and establishment of transepithelial electrical resistance is reasonable, although the rescue observed upon re-expression of PTPRK in the knockout cells was only partial. However, although in the resubmitted version, which now contains a massive amount of data, the authors addressed many of the concerns raised about the original version of the paper, they have fallen short of establishing that PTPRK-mediated dephosphorylaion of any of one the identified substrates is important for cell-cell junctions. It would strengthen the paper if they could provide evidence for this by expressing a mutant form of one (or more) of their substrates in which the PTPRK pTyr sites are mutated.

1) All the proteomic experiments were carried out with exogenously expressed PTPRK constructs. Did the authors carry also out a conventional IP/MS analysis of proteins associated with endogenous PTPRK using the anti-PTPRK mAb they have generated (an alternative would be to knock a tag into the PTPRK locus) to compare with the substrate trapping lysate pull down data and confirm interaction with the identified targets? Admittedly, this will be more challenging, but the endogenous PTPRK will be physically adjacent to likely interactors at epithelial junctions, and this could promote interactions not so readily detectable by pull downs from cell lysates where the proteins will be diluted and the contents of all the different cellular compartments will be mixed. In part their BioID data are informative in establishing that some of the candidate substrates are in the vicinity of PTPRK in the cell, but they did not use BioID to look for additional substrates for PTPRK.

2) Did the authors compare pTyr proteomes of confluent and sparse WT and knockout MCF10A cells to determine if cell-cell contact triggers PTPRK-dependent dephosphorylation events?

3) The evidence that some of the substrate-PTPRK interactions are independent of catalytic function implies, as the authors suggest, that PTPRK also has a scaffolding unction. However, they provide no insights into how these scaffolding interactions occur (i.e. what domains are involved?), and so we do not learn how important such interactions are for dephosphorylation of these substrates in the cell (or in vitro).

Reviewer #2:

This is an informative and rather heroic paper that identifies potential substrates for the membrane-bound receptor tyrosine phosphatase K (RPTPK). The authors identify and reasonably-validate a number of substrates and illustrate the complexities of tackling this problem (phosphatase-independent interactions etc). Many of these candidates are interesting proteins found at cell-cell junctions (as might be predicted from the junctional localization of RPTPK) and they include proteins, such as afadin, for which the functional consequences of dynamic phosphorylation are not well characterized. Overall, I think that the manuscript already presents a valuable resource for the community that will be the basis for future research.

Given the wealth of data that is already here, I hesitate to ask for more. But a limitation is that the authors don't have evidence for functional significance of any of the dephosphorylation events that they document. They show that RPTPK supports aspects of junctional integrity (especially barrier function) in a PTP-dependent fashion, but the impact of the manuscript would be enhanced if they could test the principle that one/some of their substrates contributes to this phenotype. The obvious candidate here is p120-catenin which they show to have increased phosphorylation on Y228 and Y904 in RPTPK KO cells. Is this hyperphosphorylation contributing to the epithelial phenotype that they document? One way to test this hypothesis would be to express Y228A/Y904A p120 in their PRPTK KO cells. (Most elegantly on a p120 RNAi background – for which there are good siRNAs available; but overexpression may be effective.)

Reviewer #3:

General comments on the manuscript:

The general interest of this manuscript to characterize specific substrates, is very important on a larger scheme of understanding RPTP (R2Bs) mechanism of action. This search for PTPRK substrates has also significant importance considering the "tumor suppressive" activities associated with PTPRK function in many cancers. It is in part answering the need to identify PTPRK substrates as potential mechanism of oncogenic development. The premises and general findings of the manuscript are of great interest in the PTP field and beyond.

Looking at the results presented, the experimental methods are well described and for the most part standard. The workflow drawings are simple and useful. Statistical analysis using anova is also appropriate for the study.

In conclusion, the manuscript is an excellent example of a comprehensive biochemical analysis of a receptor PTP and a search for physiological substrates. On this, the manuscript has interest for the readerships. Yet without a solid validation of the putative substrates into a physiological cell or animal model of diseases, the manuscript comes out short on the biological value of these findings.

Considering the rebuttal letter, four specific questions were answered by authors in this resubmission.

- Comments on answer to Question 1.

These are indeed valuable experiments. Both are difficult to generate. The first one is complicated since it is not known which substrate phospho-tyrosine site(s) would be crucial for cell -adhesion. As for the PTPRK rescue of the PTP knock-out cells, authors have already stated that the transfected PTPRK cDNA is not expressed and likely to be at various levels.

In both approaches, authors could have used various experimental design such as introducing into a safe harbor site (i.e.: AAV1,.…) the dox dependent PTPRK expression vector into the knockout cell line, and test cell-cell phenotype rescue.

A similar approach may have perhaps been attempted with the CRISPR KO of the specific substrate(s), follow by their rescue through re-expressing their cDNAs with mutated p-tyr in the same safe harbor site with dox inducible re-expression. This would then be validating the phospho-sites specific effect on cell-cell interaction. It remains that with several identified and predicted substrates' sites reported in this manuscript, this task although desirable would be major undertaking to perform.

- Comments on answer to Question 2.

On this issue, data presented are supporting that some substrates (i.e. afidin,) are indeed binding to the D2 domain in a phosphorylation independent manner and then are likely being dephosphorylated. This is a common feature of many PTP substrate recognition where other protein-protein domains anchor them to a phosphatase and then facilitate their dephosphorylation. The manuscript accurately makes a point that this is also occurring with some substrate of RPTPs.

Yet they have not identified the specific binding sites of afidin to the D2 domain. Several receptor PTPs have, like RTK, C terminal ends with additional features such as phosphorylation sites. This does not seem to be the case with the very short C-tail of the PTPRK.

- Comments on answer to Question 3

The authors' answer is unsatisfying. D2 domain for many RPTPs were tested as per their potential to trap P-Tyr proteins and there are no cases where these occur. D2 domains were associated to important regulatory functions of RPTPs such as stabilizing substrate interactions, mediating protein-protein interactions, protection against Cysteine-Oxydation and facilitating RPTP dimerization causing inhibitory phosphatase activities. A stated above, in some cases, such as PTPRE and PTPRA, the C-terminus of the RPTP provide phosphorylation dependent docking outside the D2 domain. The only solution on this issue would be to map the interactions of afidin to the D2 domain. Better of course, a structure of the PTPRK D2- afidin interaction would be ideal in understanding this mechanism. This is out of scope for this manuscript.

- Comments on answer to Question 4

The answer by authors to generate a consensus sequence is of interest particularly with the additional list of putative substrates that was generated. Yet, without validation of some of them in the KO cells/mouse… this remains speculation.

As for the statement that this effort is the first unbiased proteomic approach to identify substrates for classical PTPs, this is inaccurate as among many reports, those of Mertins et al. Mol Cell Proteomics. 2008, Lee and Bennett Methods Mol Biol. 2015, Tang et al. J. Am. Chem. Soc., 2018 are just excellent examples of such approaches.

https://doi.org/10.7554/eLife.44597.035

Author response

[Editors’ note: the author responses to the initial decision follow.]

1) What sets this paper apart is that many different proteomics approaches were used to identify proteins that appear to be substrates in vivo. The use of MCF10A knockouts and reconstituting with wildtype PTPRK or the phosphatase dead mutant is a real plus. However, what is missing is direct evidence of the importance of any of the identified PTPRK sites in cell-cell junction proteins in the integrity of cell-cell junctions, or whether D1 PTP activity is required to reverse the observed MCF10A cell phenotypes. Reviewers are bound to ask and it would not be productive send it for review only to have it rejected because the significance of the phosphatase activity isn't clear. We would not expect the relevance of individual substrates or pY sites to be established, but it is important to test whether the PTP activity is required.

We appreciate that linking alterations in signaling to the observed phenotypes will raise the impact of this work, and as you point out, would be an obvious reviewer comment. However, these experiments are particularly challenging because of a lack of expression level uniformity, which one would anticipate to be particularly important for cell-cell adhesion proteins. Nevertheless, we now include experiments that show that PTPRK partially rescues TEER and colocalization of E-Cadherin and F-actin in MCF10A PTPRK KO cells, in a phosphatase-dependent manner. Unfortunately, we could not detect induction of PTPRK in MCF10A spheroids after 14 days, which would be a key control required to interpret any changes. We conclude that phosphatase activity is an important part of the PTPRK cell adhesion phenotype, however, we also believe there is a key scaffolding function for this receptor, which is highlighted by experiments outlined below.

2) Less major points include whether the in vitro interactions with the WT PTPRK ICD or the substrate trapping mutant D1 domains were in fact dependent on pTyr residues, i.e. they did not treat the lysate with recombinant PTP prior to doing the pulldowns. A significant number of proteins bound selectively to the WT PTPRK ICD vs beads, but since the D1 catalytic domain was active, presumably these interactions were not pTyr dependent.

This is a good point and we too had assumed initially that interactions would depend on phosphotyrosine. The two traps used do have different properties, one allows the formation of a phosphocysteine intermediate (DA), the other relies on the increased affinity of enzyme for its substrate over product (CS). We agree with your analysis that binding of proteins to the WT ICD suggests phosphotyrosine is not critical for the recruitment of most substrates. There are examples in the literature, now included in our Discussion, where binding of substrates to other active, wildtype classical PTPs is observed. In the case of MAP4K4, which was trapped on the DA mutant, we have now demonstrated that this interaction can be completed by vanadate, suggesting it is trapped by phosphotyrosine. In addition, PARD3, PKP4 and p120Cat all show reduced binding to the CS trap after pulldowns from calf intestinal phosphatasetreated pervanadate lysates, again suggesting a role for phosphorylation in trapping. Surprisingly, however, we show that most substrates still bind efficiently to PTPRK domains in the absence of phosphorylation. In addition, our data support a key role for the pseudophosphatase domain in recognizing several substrates, which leads to the next issue highlighted.

3) This raises the general issue of the extent to which PTPRK interacting proteins associate directly via a target pTyr as opposed to secondary interactions, for instance those with the inactive D2 domain. In this regard, their model that D2 might recruit targets for D1 does not make much sense, unless the protein has two pTyr residues, since a pTyr bound to D2 would be protected from dephosphorylation by D1.

We had also initially anticipated that the D2 domain would function as a pTyr trap. This is because key residues in catalytic motifs of the D2 domain (HCS, WPD and Q loop) deviate from D1 sequences and resemble canonical substrate trapping mutants. Previously, the D2 domain of PTPRF (LAR) was reactivated by reverting particular sequences to those found in D1 domains. In fact, we tried exactly this with PTPRK but did not see any effect on D2 activity or binding of key substrates (data now included). This matches with recent results for PTPRE, where the D2 domain could not be reactivated by similar mutations (Lountos et al. PMID:30289412). We also noted that for existing D2 domain crystal structures, the catalytic cysteine is largely occluded (e.g. CD45; Figure 5—figure supplement 2). Unfortunately, there is not a PTPRK-family phosphatase D2 domain structure available, however, we have included a homology model that indicates significant changes in surface charge compared to the D1 such that it would be unlikely to accommodate a phosphate group. Finally, orthovanadate or lysate dephosphorylation was ineffective at depleting Afadin from the D2 domain. We think substrate recognition, in a phosphorylation-independent manner, will be an important area for future research and indicates a putative scaffolding role for these receptors, comprising dephosphorylated proteins.

4) Another issue that is not discussed is whether there is a primary sequence preference for sites dephosphorylated by D1 – they have a number of identified sites but there is no sequence comparison.

We generated a consensus sequence using our high confidence and “likely” substrates and now present a weblogo (Figure 3—figure supplement 1). The predominant trend we observe is the absence of basic residues in the pTyr-1 and pTyr+1 positions, which is consistent with the highly positively charged nature of the PTPRK active site excluding interactions with such amino acids. Similar attempts to map a substrate consensus sequence for PTP1B also show a preference for acidic or negatively charged residues N-terminal of the pTyr (Li et al. PMID: 23674824). Thus, there are probably permissive substrate primary sequences, however, given the exquisite selectivity of PTPRK it seems unlikely that primary sequence is the major specificity determinant. As an aside, we revisited work by Barr et al. (PMID: 19167335) that showed PTPRK does not dephosphorylate an EGFR-pY1068 peptide, supporting our work at the protein level where we do not observe dephosphorylation of this site. This is a particularly important negative result as EGFR-pY1068 is one of the most highly cited PTPRK substrates (Xu et al. PMID: 16263724).

In terms of significance, this is the first unbiased proteomic approach to identify substrates for a classical PTP. Our data suggest that the domains beyond the active enzyme play a key role in substrate recognition, which has also been suggested for some individual PTP substrates (e.g. Timms et al. PMID: 9632768). Our work is of high quality and provides a key step forward for the phosphatase field, by challenging general assumptions about RPTPs, for example, as thresholders of receptor tyrosine kinase signaling (e.g. Lee and Bennett PMID: 25319894) and raises the possibility that they function as core signaling scaffolds, similar to RTKs. Moreover, we have shown that PTPRK is a convincing and exciting new player in cell-cell adhesion and epithelial to mesenchymal transition. It has the potential to function as a sensor of cell contact, and associates with several known mechanotransduction molecules such as MAP4K4 and RAPGEF6. Thus, two major new questions arise from our work: How (and why) do RPTP pseudophosphatase domains recognize substrates? Is PTPRK an upstream component of mechanosensing and/or mechanotransduction pathways?

[Editors' note: the author responses to in depth peer review follow]

Reviewer #1:

[…] The identification of a small set of specific pTyr substrates for PTPRK is an advance in our understanding of this receptor PTP. The known junctional functions of the specific substrates clearly points towards a role for PTPRK in controlling cell-cell junctions, and the confirmatory evidence that PTPRK D1 catalytic activity is required for formation of proper cell-cell junctions and establishment of transepithelial electrical resistance is reasonable, although the rescue observed upon re-expression of PTPRK in the knockout cells was only partial. However, although in the resubmitted version, which now contains a massive amount of data, the authors addressed many of the concerns raised about the original version of the paper, they have fallen short of establishing that PTPRK-mediated dephosphorylaion of any of one the identified substrates is important for cell-cell junctions. It would strengthen the paper if they could provide evidence for this by expressing a mutant form of one (or more) of their substrates in which the PTPRK pTyr sites are mutated.

Although we show that PTPRK phosphatase activity is required to rescue signalling and cell adhesion phenotypes in KO cells, we agree that additional evidence showing that substrate hyperphosphorylation directly influences junctional integrity would substantially strengthen the paper. However, this would be a significant undertaking, out of scope for this initial study (as agreed by the editors). We believe this would be challenging for several reasons. There are many phosphosites requiring characterisation (> 15 upregulated in PTPRK KO cells), which may, in combination, contribute to the observed phenotypes. Therefore, rescues with phosphorylation-deficient mutant substrates might be masked by the effects of other hyperphosphorylated substrates. Moreover, some substrates have multiple phosphosites to functionally analyse, such as p120Cat where 4 phosphosites are altered in PTPRK KO cells. The ideal experiment would be to overexpress phosphomimetic mutants to see if the KO phenotypes are recapitulated on a WT background, but such mutants are unreliable for phosphotyrosine.

In an attempt to further strengthen the notion that substrate hyperphosphorylation is contributing to the PTPRK KO junctional phenotype, we have added data showing that p120Cat (hyperphosphorylated under these conditions) exhibits reduced junctional intensity by immunofluorescence in PTPRK KO vs WT MCF10A. In addition, there are several papers that have investigated the functions of some of the dysregulated sites in other settings, including p120Cat-Y228 and Y904 and Afadin Y1230, therefore we have expanded our Discussion to include these references.

1) All the proteomic experiments were carried out with exogenously expressed PTPRK constructs. Did the authors carry also out a conventional IP/MS analysis of proteins associated with endogenous PTPRK using the anti-PTPRK mAb they have generated (an alternative would be to knock a tag into the PTPRK locus) to compare with the substrate trapping lysate pull down data and confirm interaction with the identified targets? Admittedly, this will be more challenging, but the endogenous PTPRK will be physically adjacent to likely interactors at epithelial junctions, and this could promote interactions not so readily detectable by pull downs from cell lysates where the proteins will be diluted and the contents of all the different cellular compartments will be mixed. In part their BioID data are informative in establishing that some of the candidate substrates are in the vicinity of PTPRK in the cell, but they did not use BioID to look for additional substrates for PTPRK.

The PTP substrate trapping approach requires hyperphosphorylated substrates, which is readily achieved using pervanadate. IP/MS and BioID/MS approaches are less suitable than pull downs, as pervanadate would interfere with substrate binding for a D>A mutant in a cellular context. Indeed, phosphorylation of some putative PTPRK substrates was critical for successful enrichment using substrate-trapping mutants (e.g. MAP4K4 binding to the D1057A substrate-trapping mutant). However, we now know that phosphorylation-independent interactions between PTPRK and its substrates occur meaning IP/MS and BioID would identify PTP substrates. The Gingras lab has already performed a PTPRK BioID screen (St Denis et al., 2016) and reassuringly several of our PTPRK interactors (and substrates) overlap including PKP2, KIF14, DLG5, DNAJA3, PKP4, PLEKHA5 and PTPN14, despite the use of different cell lines. Recently, IP/MS was also used to identify PTP interactors (Kumar P et al., 2017) in HEK293T cells. This is a less favourable approach for the receptor PTPs due to compromises between solubility and preserving interactions. Indeed, Kumar et al. did not enrich for junctional interactors for PTPRM by IP/MS from HEK293T cells, however, PTPRU interacted with some junctional proteins including Afadin. Overall, the number of interactors is notably fewer for PTPRM and PTPRU than we find for PTPRK. Our main aim was to identify high-confidence substrates for PTPRK, however, we agree that a combination of approaches, in different cell lines, would identify additional substrate candidates.

2) Did the authors compare pTyr proteomes of confluent and sparse WT and knockout MCF10A cells to determine if cell-cell contact triggers PTPRK-dependent dephosphorylation events?

We did not do this experiment; however, it is an interesting suggestion. Wild type MCF10A cells experience cell-cell contact when subconfluent, tending to grow in tightly associated ‘islands’ that collectively migrate to form a confluent monolayer. PTPRK localises to filopodial contacts between individual cells. In line with the presence of PTPRK at early contacts, we note that PTPRK KO cells do not coalesce to the same extent as wildtype cells (see Author response image 1), suggesting an early adhesion defect. It is therefore likely that signaling differences are occurring even at this early stage and would be worth analysing, with the caveat that contact-mediated kinase signaling (e.g. Eph receptors) might be compromised at low confluence.

3) The evidence that some of the substrate-PTPRK interactions are independent of catalytic function implies, as the authors suggest, that PTPRK also has a scaffolding unction. However, they provide no insights into how these scaffolding interactions occur (i.e. what domains are involved?), and so we do not learn how important such interactions are for dephosphorylation of these substrates in the cell (or in vitro).

We do provide evidence that the D2 domains of PTPRK and PTPRM can determine interaction specificity (NUFIP2, Afadin), however, we concede that the domains of PTPRK substrates that determine their interactions have not been mapped. These will be important future experiments to understand the full range of signalling that can be mediated by these receptors through their substrates and interaction partners.

Reviewer #2:

[…] Given the wealth of data that is already here, I hesitate to ask for more. But a limitation is that the authors don't have evidence for functional significance of any of the dephosphorylation events that they document. They show that RPTPK supports aspects of junctional integrity (especially barrier function) in a PTP-dependent fashion, but the impact of the manuscript would be enhanced if they could test the principle that one/some of their substrates contributes to this phenotype. The obvious candidate here is p120-catenin which they show to have increased phosphorylation on Y228 and Y904 in RPTPK KO cells. Is this hyperphosphorylation contributing to the epithelial phenotype that they document? One way to test this hypothesis would be to express Y228A/Y904A p120 in their PRPTK KO cells. (Most elegantly on a p120 RNAi background – for which there are good siRNAs available; but overexpression may be effective.)

Please see comments addressing a similar point from reviewer #1. This is a great suggestion, however, one of the challenges we could anticipate is achieving similar levels of expression in neighbouring confluent cells to achieve a rescue of junctional integrity. Constructs for p120Cat with phosphorylation-deficient mutants at Y174, Y228, Y904 and Y865 would have to be stably integrated via lentiviral transduction or introduced via a safe harbour site (as suggested by reviewer #3) into PTPRK KO MCF10A cells. This experiment has been done in part demonstrating that phosphorylation deficient mutants affecting tyrosines 112, 228, 257, 280, 291, 296, 302 could rescue p120Cat null adhesion phenotypes (Mariner et al., 2004). This is at least consistent with the idea that dephosphorylated p120Cat promotes adhesion. It might be simpler to test the impact of Y1230F on Afadin. However, Afadin knockdown has a dramatic impact on cell-cell adhesion meaning the mutant form would have to rescue this first, which might make interpreting PTPRK KO junctional phenotypes challenging. Furthermore, Afadin is a large protein (>1800 AAs) presenting additional challenges with cell line generation.

Reviewer #3:

[…] Considering the rebuttal letter, four specific questions were answered by authors in this resubmission.

- Comments on answer to “However, what is missing is direct evidence of the importance of any of the identified PTPRK sites in cell-cell junction proteins in the integrity of cell-cell junctions, or whether D1 PTP activity is required to reverse the observed MCF10A cell phenotypes.”.

These are indeed valuable experiments. Both are difficult to generate. The first one is complicated since it is not known which substrate phospho-tyrosine site(s) would be crucial for cell -adhesion. As for the PTPRK rescue of the PTP knock-out cells, authors have already stated that the transfected PTPRK cDNA is not expressed and likely to be at various levels.

In both approaches, authors could have used various experimental design such as introducing into a safe harbor site (i.e.: AAV1,.…) the dox dependent PTPRK expression vector into the knockout cell line, and test cell-cell phenotype rescue.

A similar approach may have perhaps been attempted with the CRISPR KO of the specific substrate(s), follow by their rescue through re-expressing their cDNAs with mutated p-tyr in the same safe harbor site with dox inducible re-expression. This would then be validating the phospho-sites specific effect on cell-cell interaction. It remains that with several identified and predicted substrates' sites reported in this manuscript, this task although desirable would be major undertaking to perform.

For rescue experiments, although our lentiviral stable cell lines were sorted by flow cytometry based on their expression levels, there was still intercellular variability that could have influenced the degree of rescue achievable. A safe harbour might have been a good alternative, however, the size of these cDNAs makes them challenging to engineer into cell lines. We have also found that the PTPRK cDNA is susceptible to recombination. We agree that attempting to understand the contributions of the individual substrate sites would be informative, but also a major undertaking beyond the scope of this manuscript, as described in the comments to reviewers #1 and #2.

- Comments on answer to “whether the in vitro interactions with the WT PTPRK ICD or the substrate trapping mutant D1 domains were in fact dependent on pTyr residues, i.e. they did not treat the lysate with recombinant PTP prior to doing the pulldowns. A significant number of proteins bound selectively to the WT PTPRK ICD vs beads, but since the D1 catalytic domain was active, presumably these interactions were not pTyr dependent.”.

On this issue, data presented are supporting that some substrates (i.e. afidin,) are indeed binding to the D2 domain in a phosphorylation independent manner and then are likely being dephosphorylated. This is a common feature of many PTP substrate recognition where other protein-protein domains anchor them to a phosphatase and then facilitate their dephosphorylation. The manuscript accurately makes a point that this is also occurring with some substrate of RPTPs.

Yet they have not identified the specific binding sites of afidin to the D2 domain. Several receptor PTPs have, like RTK, C terminal ends with additional features such as phosphorylation sites. This does not seem to be the case with the very short C-tail of the PTPRK.

As the reviewer points out, there are limited additional sequence features beyond the PTPRK D2 domain, suggesting that substrates, such as Afadin, may be binding to surfaces on the domain itself. An interesting future question is why these receptors possess pseudo-phosphatase domains rather than other protein-protein interaction domains, such as PDZ-binding domains present in, for example, Eph receptors.

- Comments on answer to “In this regard, their model that D2 might recruit targets for D1 does not make much sense, unless the protein has two pTyr residues, since a pTyr bound to D2 would be protected from dephosphorylation by D1.”

The authors' answer is unsatisfying. D2 domain for many RPTPs were tested as per their potential to trap P-Tyr proteins and there are no cases where these occur. D2 domains were associated to important regulatory functions of RPTPs such as stabilizing substrate interactions, mediating protein-protein interactions, protection against Cysteine-Oxydation and facilitating RPTP dimerization causing inhibitory phosphatase activities. A stated above, in some cases, such as PTPRE and PTPRA, the C-terminus of the RPTP provide phosphorylation dependent docking outside the D2 domain. The only solution on this issue would be to map the interactions of afidin to the D2 domain. Better of course, a structure of the PTPRK D2- afidin interaction would be ideal in understanding this mechanism. This is out of scope for this manuscript.

The R2B family D2 domain has not yet been characterized structurally, we therefore did not want to make any assumptions about the nature of the interactions. A previous study showed that the PTPRF/LAR D2 domain could be reactivated by mutations in two motifs (Nam et al., 1999) suggesting that its catalytic cysteine is accessible to phosphotyrosine. Indeed, studies on DLAR suggest its D2 domain binds phosphopeptides (Madan et al., 2011). The PTPRK D2 domain possesses a WPD>WAS mutation in its WPD-Loop, resembling a D>A substrate trapping mutant. However, as pointed out, this is not the mechanism for D2 domain recognition of substrates, which remains an open question. A co-crystal structure is an important future goal, first requiring domain mapping experiments, for example, with Afadin as suggested by reviewer #1.

- Comments on answer to “Another issue that is not discussed is whether there is a primary sequence preference for sites dephosphorylated by D1 – they have a number of identified sites but there is no sequence comparison.”

The answer by authors to generate a consensus sequence is of interest particularly with the additional list of putative substrates that was generated. Yet, without validation of some of them in the KO cells/mouse… this remains speculation.

Although the reviewer suggests that the outcome of this analysis is speculative, it agrees with previous studies that show limited specificity at the sequence level for several PTPs (e.g. Barr et al., 2009). We agree that more validated PTP substrates are required to establish this.

As for the statement that this effort is the first unbiased proteomic approach to identify substrates for classical PTPs, this is inaccurate as among many reports, those of Mertins et al. Mol Cell Proteomics. 2008, Lee and Bennett Methods Mol Biol. 2015, Tang et al. J. Am. Chem. Soc., 2018 are just excellent examples of such approaches.

This is an incorrect statement on our part, and was not intended to diminish the efforts of numerous previous studies. However, we do believe this is the first of such approaches to identify and validate substrates for the R2B RPTP subfamily. Thank you for allowing us to clarify.

https://doi.org/10.7554/eLife.44597.036

Article and author information

Author details

  1. Gareth W Fearnley

    Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
    Contribution
    Conceptualization, Validation, Investigation, Visualization, Methodology, Writing—review and editing
    Competing interests
    No competing interests declared
  2. Katherine A Young

    Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
    Contribution
    Investigation, Visualization, Methodology, Writing—review and editing
    Competing interests
    No competing interests declared
  3. James R Edgar

    1. Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
    2. Department of Pathology, University of Cambridge, Cambridge, United Kingdom
    Contribution
    Investigation, Methodology
    Competing interests
    No competing interests declared
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7903-8199
  4. Robin Antrobus

    Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
    Contribution
    Formal analysis, Visualization, Methodology, Project administration
    Competing interests
    No competing interests declared
  5. Iain M Hay

    Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
    Contribution
    Resources, Methodology, Writing—review and editing
    Competing interests
    No competing interests declared
  6. Wei-Ching Liang

    Antibody Engineering Department, Genentech, South San Francisco, United States
    Contribution
    Formal analysis, Methodology
    Competing interests
    Employed by Genentech and own Roche shares.
  7. Nadia Martinez-Martin

    Microchemistry, Proteomics and Lipidomics Department, Genentech, South San Francisco, United States
    Contribution
    Investigation, Methodology
    Competing interests
    Employed by Genentech and own Roche shares.
  8. WeiYu Lin

    Antibody Engineering Department, Genentech, South San Francisco, United States
    Contribution
    Formal analysis, Methodology
    Competing interests
    Employed by Genentech and own Roche shares.
  9. Janet E Deane

    Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
    Contribution
    Supervision, Methodology
    Competing interests
    No competing interests declared
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4863-0330
  10. Hayley J Sharpe

    Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
    Contribution
    Conceptualization, Formal analysis, Supervision, Funding acquisition, Validation, Investigation, Visualization, Methodology, Writing—original draft, Project administration, Writing—review and editing
    For correspondence
    hjs49@cam.ac.uk
    Competing interests
    No competing interests declared
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4723-298X

Funding

Wellcome and Royal Society (Sir Henry Dale Fellowship: 109407)

  • Gareth W Fearnley
  • Hayley J Sharpe

Royal Society (100371)

  • Janet E Deane

Cancer Research UK (PhD Studentship)

  • Katherine A Young

Wellcome (086598)

  • James R Edgar

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Acknowledgements

We thank FJ de Sauvage, A-C Gingras, V Pham, J Lill, D Ron and M Weekes for reagents and expertise; M Gratian and M Bowen for microscopy expertise; the CIMR flow cytometry core facility, in particular R Schulte and C Cossetti for their advice and support in cell sorting; G Griffiths, D Larrieu, S Munro, and A Schuldt for critical reading of the manuscript. This work was supported by a Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (109407) awarded to HJS and a Wellcome Trust (100140) grant awarded to CIMR. JED is funded by a Royal Society fellowship (100371). JRE is supported by a Wellcome Trust grant (086598). KAY is supported by a CRUK PhD studentship and IMH is supported by a CIMR PhD studentship.

Senior Editor

  1. Jonathan A Cooper, Fred Hutchinson Cancer Research Center, United States

Reviewing Editor

  1. Tony Hunter, Salk Institute for Biological Studies, United States

Reviewers

  1. Tony Hunter, Salk Institute for Biological Studies, United States
  2. Alpha Yap, University of Queensland, Australia
  3. Michel Tremblay, McGill University

Publication history

  1. Received: December 20, 2018
  2. Accepted: March 23, 2019
  3. Version of Record published: March 29, 2019 (version 1)

Copyright

© 2019, Fearnley et al.

This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

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