Arginine Methylation of SHANK2 by PRMT7 Promotes Human Breast Cancer Metastasis Through Activating Endosomal FAK Signalling

This article has been retracted. Read the retraction notice

RESEARCH ARTICLE

Arginine methylation of SHANK2 by PRMT7 promotes human breast cancer metastasis through activating endosomal FAK signalling Yingqi Liu1, Lingling Li2, Xiaoqing Liu1, Yibo Wang3, Lingxia Liu2, Lu Peng2, Jiayuan Liu2, Lian Zhang1, Guannan Wang1, Hongyuan Li3, Dong-Xu Liu4, Baiqu Huang1, Jun Lu2*, Yu Zhang1*

1The Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, China; 2The Institute of Genetics and Cytology, Northeast Normal University, Changchun, China; 3Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China; 4The Centre for Biomedical and Chemical Sciences, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand

Abstract Arginine methyltransferase PRMT7 is associated with human breast cancer metastasis. Endosomal FAK signalling is critical for cancer cell migration. Here we identified the pivotal roles of PRMT7 in promoting endosomal FAK signalling activation during breast cancer metastasis. PRMT7 exerted its functions through binding to scaffold protein SHANK2 and catalyzing di-methylation of SHANK2 at R240. SHANK2 R240 methylation exposed ANK domain by disrupting its SPN-ANK domain blockade, promoting in co-accumulation of dynamin2, talin, FAK, cortactin with SHANK2 on endosomes. In addition, SHANK2 R240 methylation activated endosomal FAK/cortactin signals in *For correspondence: vitro and in vivo. Consistently, all the levels of PRMT7, methylated SHANK2, FAK Y397 [email protected] (JL); phosphorylation and cortactin Y421 phosphorylation were correlated with aggressive clinical breast [email protected] (YZ) cancer tissues. These findings characterize the PRMT7-dependent SHANK2 methylation as a key player in mediating endosomal FAK signals activation, also point to the value of SHANK2 R240 Competing interests: The methylation as a target for breast cancer metastasis. authors declare that no competing interests exist. Funding: See page 19 Received: 06 April 2020 Introduction Accepted: 25 August 2020 Protein arginine methyltransferases (PRMTs) catalyze mono-methylation and symmetric or asymmet- Published: 26 August 2020 ric di-methylation of arginine residues on both histone and non-histone substrates to modulate diverse biological processes, including transcription, cell signalling, mRNA translation, DNA damage Reviewing editor: Lynne-Marie Postovit, University of Alberta, repair signalling, receptor trafficking, protein stability and pre-mRNA splicing (Jelinic et al., Canada 2006; Bedford and Clarke, 2009; Dhar et al., 2012; Jeong et al., 2016; Blanc and Richard, 2017; Jeong et al., 2020). Protein Arginine Methyltransferase 7 (PRMT7) was reported as a type III PRMT Copyright Liu et al. This article to catalyze mono-methylation of arginine residues on both histone and non-histone substrates is distributed under the terms of (Bedford and Clarke, 2009; Karkhanis et al., 2012; Blanc and Richard, 2017; Jain and Clarke, the Creative Commons Attribution License, which 2019; Haghandish et al., 2019). Recent studies also reported that PRMT7 can symmetrically di- permits unrestricted use and methylate proteins such as p38 and GLI2 (Jeong et al., 2020; Vuong et al., 2020). Others and our redistribution provided that the previous studies have linked PRMT7 to breast cancer progression. Specifically, our previous work original author and source are reported that PRMT7 promoted metastasis of breast carcinoma cells by triggering EMT (epithelial- credited. mesenchymal transition) program (Yao et al., 2014). PRMT7 can also upregulate the expression of

Liu et al. eLife 2020;9:e57617. DOI: https://doi.org/10.7554/eLife.57617 1 of 27 This article has been retracted. Read the retraction notice Research article Cancer Biology Cell Biology matrix metalloproteinase nine to promote metastasis of breast cancer (Baldwin et al., 2015). We also found that PRMT7 was automethylated at residue R531, which potentiated the PRMT7-induced EMT program and metastasis (Geng et al., 2017). Endocytosis of migrating cells is a fundamental process which is required for adhesion formation and efficient cell movement (Kaksonen and Roux, 2018; Scita and Di Fiore, 2010). Increasing evidence indicates that deregulated endocytosis is a relapse mechanism that contributes to the acquisition of malignant characteristics in tumour cells, including enhanced cell migration, invasion and metastasis (Hamidi and Ivaska, 2018; McMahon and Boucrot, 2011). During invasive cell migration, receptors are internalized through the cyclic trafficking of endosome and transported to early endosome before recycling back to the plasma membrane, consequently the cytoskeleton is polar- ized by actin polymerization via scaffold proteins, and forming a leading protrusion (Trusolino et al., 2010; Wang et al., 2011; Verma et al., 2015; Hamidi and Ivaska, 2018). The focal adhesion kinase (FAK) is a cytoplasmic protein-tyrosine kinase and plays a pivotal role in many cellular processes such as cell adhesion, survival and migration (Murphy and Courtneidge, 2011; Alanko and Ivaska, 2016; Schoenherr et al., 2018). During endocytosis, integrin or talin engages with FAK to co-localize on endosome. FAK undergos autophosphorylation on Y397, which results in cell dissemination (Alanko et al., 2015; Nader et al., 2016; Xiuping et al., 2018; Hamidi and Ivaska, 2018). Addition- ally, Y397 phosphorylation of FAK facilitates the association of FAK with actin-binding protein cortactin, which renders cortactin function in formation of lamellipodia and filopodia (Tomar et al., 2012; Eke et al., 2012; Wang et al., 2011). Although increased endosome recycling to the plasma membrane contributes to enhanced cell migration, the mechanism of endosomal assembly and signals activation is largely unknown. Recent reports also uncovered the connection between arginine methylation and phosphorylation with endocytic trafficking (Albrecht et al., 2018). However, whether PRMT7 promotes breast cancer metastasis through regulating endocytic traffic remains unclear. Scaffolding proteins SH3 and multiple ankyrin repeat domains 2 (SHANK2) localizes in cytoplasm and plays important roles in regulating synapse plasticity (Lee et al., 2010; Naisbitt et al., 1999; Sala et al., 2001; Sheng and Kim, 2000; Tu et al., 1999). The SHANK family of master scaffolding proteins include three members, that is SHANK1, 2 and 3. SHANK family proteins have been linked to Autistic Spectrum Disorder (Lim et al., 1999; Mei et al., 2016; Monteiro and Feng, 2017; Yoon et al., 2017). Mutations in genes encoding SHANK family proteins (SHANK1, 2 and 3) often result in marked behavioural phenotypes in mice (Mameza et al., 2013; Schmeisser et al., 2012; Won et al., 2012), such as an increase in repetitive routines, altered social behaviour and anxiety- like phenotypes. Recent studies also linked SHANK family proteins to cancer cell invasion. SHANK1 and SHANK3 were reported to inhibit cell spreading, migration and invasion in cancer cells through sequestering active Rap1 and R-Ras (Lilja et al., 2017). However, the precise roles of SHANK2 in tumour progression have not been investigated. In this study, we identified that SHANK2 was a new substrate of PRMT7. Methylation of SHANK2 at R240 by PRMT7 exposed ANK domain by disrupting its SPN-ANK domain blockade. Further, SHANK2 R240 methylation reinforced breast cancer cell migration through activating endosome FAK signalling. Collectively, these findings represent one mechanistic explanation for how PRMT7 regulating breast cancer cell metastasis by mediating endosome formation, and may provide potential clues for tumour metastasis treatment strategies.

Results SHANK2 interacts with PRMT7 and is a substrate for PRMT7-mediated arginine methylation To explore the mechanism of PRMT7 action in tumour metastatic progression, we used the Flag- tagged PRMT7 fusion protein as bait in mass spectrometry to pick up the possible regulatory factors, which might be directly regulated by PRMT7 (Figure 1A). The results revealed that PRMT7 is associated with multiple proteins including SHANK2, MRPS23, Plectin1, SNRPB and ARHGAP32. Among the PRMT7-interacting proteins, we chose SHANK2 as a target for a more detailed study. Although SHANK1 and SHANK3 have been reported to inhibit cancer cell migration (Lilja et al., 2017), whether SHANK2 plays a role in cancer progression is unknown. To determine whether PRMT7 methylates SHANK2, we first conducted a CoIP assay to confirm the binding between

Liu et al. eLife 2020;9:e57617. DOI: https://doi.org/10.7554/eLife.57617 2 of 27 This article has been retracted. Read the retraction notice Research article Cancer Biology Cell Biology

Figure 1. PRMT7 methylated SHANK2. Immunoprecipitation and immunoblotting analyzes were performed with the indicated antibodies. (A) PRMT7 associated proteins from MCF7 cells expressing stable FLAG-PRMT7 were immunopurified with anti-FLAG (a-FLAG) affinity resins. The protein bands were analyzed by mass spectrometry. Representative peptide fragments of PRMT7 associated proteins and peptide coverage of the indicated proteins are shown. (B) HEK293T cells were co-transfected with Flag-PRMT7 and/or HA-SHANK2 plasmids. (C) Endogenous SHANK2 or PRMT7 was IP from MDA-MB-231 cells lysate, with anti-SHANK2 or anti-PRMT7 antibody, and the binding of PRMT7 and SHANK2 was examined by western blot. (D) Purified bacterially expressed GST or GST-PRMT7 was incubated with MDA-MB-231 cells lysate. GST-pulldown assay showed direct interaction between SHANK2 and recombinant PRMT7. (E) Diagram of the domains in SHANK2 protein. The schematics of the GST-SHANK2 expression plasmid, as well as domains and truncated mutants. (F) SHANK2 truncated mutants were incubated with MDA-MB-231 cells lysate. GST-pulldown assay showed direct interaction between PRMT7 and recombinant SHANK2. (G) HEK293T cells were transfected with increasing amounts of Flag-PRMT7 expression plasmids. Immunoprecipitation of SHANK2 with anti-SHANK2 antibody was performed. (H) MDA-MB-231 with or without stable expression of the indicated PRMT7 shRNA or a control shRNA. Immunoprecipitation of SHANK2 with anti-SHANK2 antibody was performed. (I) MDA-MB-231 cells with or without expressing PRMT7 shRNA and with or without reconstituted expression of WT PRMT7 or PRMT7 enzymatic activity mutant. Immunoprecipitation of SHANK2 with anti-SHANK2 antibody was performed. (J) HA-tagged SHANK2 was expressed in HEK293T cells. HA-purified SHANK2 protein was incubated with SAM and with or without purified bacterially expressed PRMT7. Methylation of recombinant SHANK2 protein was determined by western blot. The online version of this article includes the following figure supplement(s) for figure 1: Figure supplement 1. SHANK2 di-methylation was dependent on PRMT7.

PRMT7 and SHANK2 (Figure 1B and C). We then incubated the purified GST-tagged PRMT7 with SHANK2 protein, and the results showed that they could interact with each other (Figure 1D). To map the SHANK2 regions that bind PRMT7, we expressed a series of truncated GST- SHANK2 (Figure 1E), and found that the SHANK2 ANK, PDZ and SAM domains were responsible for the interaction between PRMT7 and SHANK2 (Figure 1F). The interaction between PRMT7 and SHANK2 indicated that SHANK2 might be a new substrate of PRMT7. Next, we determine whether PRMT7 is involved in regulation of SHANK2 methylation. By using methylation assay, we found that overexpression of PRMT7 resulted in increased symmetric arginine di-methylation of SHANK2 in HEK293T cells (low level of PRMT7) (Figure 1G). In addition, we

Liu et al. eLife 2020;9:e57617. DOI: https://doi.org/10.7554/eLife.57617 3 of 27 This article has been retracted. Read the retraction notice Research article Cancer Biology Cell Biology constructed lentiviral vectors containing shRNAs targeting the CDS of PRMT7 to knock down the endogenous PRMT7 of MDA-MB-231 cells. SHANK2 di-methylation level was reduced upon PRMT7 depletion, and the reduced di-methylation of SHANK2 was restored by the reconstituted expression of WT PRMT7 (PRMT7 WT) but not by mutant PRMT7 at its enzymatic domain (PRMT7 Mut) in MDA- MB-231 cells (high level of PRMT7) (Figure 1H and I). Meanwhile, SHANK2 di-methylation level was attenuated by the reconstituted expression of WT PRMT7 (PRMT7 WT) but not of mutant PRMT7 at its auto-methylation residue (PRMT7 R531 mutant) in PRMT7 depleted MDA-MB-231 cells (Fig- ure 1—figure supplement 1). To further confirm PRMT7 directly methylated SHANK2, we used purified GST-PRMT7 and HA-SHANK2 for in vitro methylation assay followed by incubation with SAM (the methyl donor). Apparently, incubation of recombinant PRMT7 and SHANK2 gave rise to a remarkable increase in methylation of SHANK2 in the presence of SAM, while SHANK2 methylation was undetectable in the absence of SAM (Figure 1J). These results suggest that PRMT7 physically interacts with and methylates SHANK2.

PRMT7 methylates SHANK2 at R240 residue To further identify the methylation site of SHANK2, we performed mass spectrometric analysis using malignant breast cancer cell MDA-MB-231 lysate with overexpressed Rat HA-SHANK2 (a gift from Dr. Min Goo Lee). We identified that the arginine 240 residue (R240) of SHANK2 was di-methylated (Figure 2A). Using sequence homology comparison, we found that the R240 residue of SHANK2 is evolutionarily conserved (Figure 2B). To determine whether SHANK2 R240 residue was methylated by PRMT7, we constructed lentiviral vectors containing shRNAs targeting the 3’UTR of SHANK2 to knock down the endogenous SHANK2 of MDA-MB-231 cells. Then, we transfected SHANK2 wild-

Figure 2. PRMT7 methylated SHANK2 at R240. (A) The purified SHANK2 from MDA-MB-231 cells transfected with HA-SHANK2 was analyzed for methylation by mass spectrometry. The SHANK2 R240 residue in fragmentation of KAARMRN was methylated. The Mascot score was 27.28, and the expectation value was 3.74E-04. (B) Alignment of the consensus SHANK2 sequences between different species near the R240 methylation site. (C) MDA-MB-231 cells with or without expressing SHANK2 shRNA and with or without reconstituted expression of WT SHANK2 or SHANK2 R240K mutant. Immunoprecipitation of HA with anti-HA antibody was performed. (D) Flag-tagged SHANK2 WT or SHANK2 R240K was transfected into MDA-MB-231 cells. HA-purified SHANK2 WT or SHANK2 R240K proteins were incubated with purified bacterially expressed PRMT7 and SAM. Methylation of SHANK2 protein was determined by western blot. (E) HEK293T cells were co-transfected with increasing amounts of Flag-PRMT7 and SHANK2 WT or SHANK2 R240K expression plasmids. Immunoprecipitation of SHANK2 with anti-SHANK2 antibody was performed. The online version of this article includes the following figure supplement(s) for figure 2: Figure supplement 1. The role of PRMT5 in PRMT7 mediated SHANK2 methylation.

Liu et al. eLife 2020;9:e57617. DOI: https://doi.org/10.7554/eLife.57617 4 of 27 This article has been retracted. Read the retraction notice Research article Cancer Biology Cell Biology type or SHANK2 mutation with R240 residue replaced by lysine (SHANK2 R240K) into endogenous SHANK2 depleted MDA-MB-231 cells. We found that di-methylation level of SHANK2 R240K was lower when compared to SHANK2 WT in MDA-MB-231 cells (Figure 2C and D). We then overexpressed increasing doses of PRMT7 in HEK293T cells, and we found that SHANK2 R240 di-methylation level was increased accordingly (Figure 2E). PRMT5 has been reported to interact with PRMT7. We then examined the effect of PRMT5 overexpression on SHANK2 R240 di-methylation in HEK293T cells. We found that dosage dependent expression of PRMT5 did not increase the di- methylation at SHANK2 R240 (Figure 2—figure supplement 1A and B). Furthermore, we examined the effect of PRMT5 inhibitors (GSK591) on SHANK2 di-methylation (Fedoriw et al., 2019). We found that even when PRMT5 activity was inhibited, overexpression of PRMT7 could still increase the SHANK2 di-methylation level both in HEK293T and MDA-MB-231 cells (Figure 2—figure supplement 1C and D). Thus, although PRMT5 and PRMT7 existed in the same complex, our data indicated that di-methylation of SHANK2 R240 was mainly mediated by PRMT7. Taken together, these results indicate that PRMT7 physically interacts with SHANK2 to methylate R240 residue of SHANK2.

SHANK2 R240 methylation potentiates breast cancer cell migration and invasion Previous reports showed that expression of SHANK2 gene was higher in head and neck cancer tissues than that in adjacent tissues, and this upregulation was positively correlated with the survival rate and prognosis of the patients (Qin et al., 2016). Consistently, we also observed that SHANK2 mRNA was highly expressed in human breast tumours (Figure 3A). To further investigate the clinical relevance of SHANK2 methylation with breast cancer, a direct western blot analysis of several subtypes of human breast cancer tumours was performed. The results demonstrated that SHANK2 methylation level was significantly higher in luminal B Her2(+) and Triple-negative breast cancer samples, than that in normal, luminal A and luminal B Her2(-) samples, which implicated a positive correlation between SHANK2 methylation and high metastatic potential (Figure 3B–E). In addition, to determine the relationship between PRMT7-mediated SHANK2 R240 methylation and metastasis, we analyzed the correlation between PRMT7 and the stage of breast cancer patients through TCGA Breast (BRCA) database. Among 1075 breast cancer patients, 89 out of 847 PRMT7 low-expression breast cancer patients were stage III or IV (10.5%), while 63 out of 228 PRMT7 high-expression breast cancer patients were stage III or IV (27.6%) (Figure 3—figure supplement 1). These data indicated that the expression of PRMT7 was positively correlated with the proportion of patients with stage III or IV breast cancer, which predicted poor prognosis. Next, we intended to study the effects of SHANK2 di-methylation on breast cancer cells. Out of 6 cell lines analyzed, high metastatic potential breast cancer cells (BT549 and MDA-MB-231) exhibited high SHANK2 di-methylation levels, whereas normal mammary epithelial cell (MCF10A), low metastatic potential breast cancer cell (MCF7, BT474 and T47D) showed relatively low SHANK2 di-methylation level (Figure 3F and G). Furthermore, we analyzed the expression profile of EMT-associated markers, and found that the epithelial marker ZO-1 was increased, while the mesenchymal markers Fibronectin and N-cadherin were decreased upon SHANK2 depletion; meanwhile, ZO-1 expression was decreased while Fibronectin and N-cadherin expressions were restored by reconstituted expression of SHANK2 WT but not of SHANK2 R240K in MDA-MB-231 and BT549 cells (Figure 3H and Figure 3—figure supplement 2A). However, SHANK2 did not induce EMT program in SHANK2 overexpressed MCF10A cells or in SHANK2 depleted MDA-MB-231 cells (Figure 3—figure supplement 2B and C). In addition, MMP2/ MMP9 activation was inhibited by SHANK2 depletion, while the inhibition was abrogated by reconstituted expression of SHANK2 WT but not of SHANK2 R240K (Figure 3I), and the migration/invasion capabilities of MDA-MB-231 cells were also inhibited by SHANK2 depletion, and in both cases the inhibition was abrogated by reconstituted expression of SHANK2 WT but not of SHANK2 R240K (Figure 3J and K). Metastatic tumour cells are often accompanied by stem cell characteristics; however, we did not identify CD44high/CD24low cell populations in SHANK2 depleting MDA-MB-231 or SHANK2-expressing MCF10A cells tested by FACS (Figure 3—figure supplement 2D). Together, these results strongly support the assumption that SHANK2 di-methylation is a crucial factor control- ling EMT, migration and invasion characteristics of breast cancer cells.

Liu et al. eLife 2020;9:e57617. DOI: https://doi.org/10.7554/eLife.57617 5 of 27 This article has been retracted. Read the retraction notice Research article Cancer Biology Cell Biology

Figure 3. SHANK2 R240 methylation promoted migration and invasion of breast cancer cells. (A) Comparison of SHANK2 expression level in breast cancer tissues of different breast cancer subtypes with that in normal tissues by RT-PCR. The logarithmic scale of 2-DDCt was used to measure the fold- change. b-actin was used as an internal reference. n = 27, *p<0.05, **p<0.01, ***p<0.001, one-way ANOVA test. (B–E) Comparison of PRMT7, SHANK2 and di-methylated SHANK2 levels in breast cancer tissues using western blot analysis. Data are based on the analysis of independent samples (n = 27). Figure 3 continued on next page

Liu et al. eLife 2020;9:e57617. DOI: https://doi.org/10.7554/eLife.57617 6 of 27 This article has been retracted. Read the retraction notice Research article Cancer Biology Cell Biology

Figure 3 continued Immunoprecipitation of SHANK2 with anti-SHANK2 antibody was performed. *p<0.05, **p<0.01, ***p<0.001, ns = not significant, one-way ANOVA test. (F) SHANK2 mRNA expression in indicated breast cancer cell lines by RT-PCR. The logarithmic scale of 2-DDCt was used to measure the fold-change. b- actin was used as an internal reference. ***p<0.001, Student’s t test. (G) SHANK2 was IP from indicated breast cancer cell lines lysate, and input lysates and IP samples were analyzed using anti-methylation, anti-SHANK2 or anti-PRMT7 antibodies, as indicated. (H) MDA-MB-231 cells expressing SHANK2 shRNA and reconstituted expression of SHANK2 WT or SHANK2 R240K mutant. Western blot was performed with the indicated EMT marker antibodies. (I) MDA-MB-231 cells with or without stable expression of the indicated SHANK2 shRNA were transfected with SHANK2 WT or SHANK2 R240K mutant. Assessment of MMP2 and MMP9 enzymatic activities by gelatin zymography. (J and K) MDA-MB-231 cells expressing SHANK2 shRNA and reconstituted expression of SHANK2 WT or SHANK2 R240K mutant. Cell migration (J) and Invasion (K) were determined by transwell assays. (n = 3, independent experiments). Scale bars: 100 mm. Data represent the mean ± SD of three independent experiments. ***p<0.001, Student’s t test. The online version of this article includes the following figure supplement(s) for figure 3: Figure supplement 1. PRMT7 was associated with clinical outcomes. Figure supplement 2. SHANK2 was involved in breast cancer cells EMT.

R240 methylation disturbs SPN-ANK domain blockade of SHANK2 To explore the mechanism of SHANK2 methylation in breast cancer cell migration and invasion, we studied the conformational changes of wild-type SHANK2 (WT), di-methylated SHANK2 at R240 (Dimethyl R240), and its mutant (R240K) by using molecular dynamics simulations (Kumar et al., 1992; Phillips et al., 2005; Vanommeslaeghe et al., 2010; Zhu and Hummer, 2012; Huang and MacKerell, 2013; Wang et al., 2016; Waterhouse et al., 2018; Grossfield, 2020). As shown in

Figure 4. R240 methylation impaired SPN-ANK domain interaction of SHANK2. (A) Definition of the SPN domain (coloured in green) and the ANK domain (coloured in cyan) in SHANK2. The location of R240 was represented with sticks. (B) Key residues forming hydrogen bonds between SPN and ANK in SHANK2 WT. R240 can form hydrogen bonds with H236 in ANK (coloured in magenta). (C) Key residues forming hydrogen bonds between SPN and ANK in SHANK2 R240K. K240 can still form hydrogen bonds with H236 in ANK (coloured in magenta). (D) Potential of mean forces for the conformational changes (from closed state to the open state) of SPN and ANK in the wild type (WT, black line), methylated (Dimethyl R240, blue line) and mutant (R240K, red line) SHANK2.

Liu et al. eLife 2020;9:e57617. DOI: https://doi.org/10.7554/eLife.57617 7 of 27 This article has been retracted. Read the retraction notice Research article Cancer Biology Cell Biology Figure 4A, the SPN domain in Dimethyl R240 needs less energy to reach an ‘open’ state than that in SHANK2 WT and R240K, according to the free energy profile. To further investigate how the dime- thylated R240 affects the conformational changes between SPN and ANK domains, the trajectory for the window with the global minimum free energy (the distance between SPN and ANK is 31.5 A˚ , the SPN and ANK domains were represented in different colours in Figure 4B) in WT, the one (the distance between SPN and ANK is 32 A˚ ) in Dimethyl R240 and the one (the distance between SPN and ANK is 30 A˚ ) in R240K were analysed. R240 can form hydrogen bonds with its neighbouring residue H236 and by this R240 remotely influences the interactions between SPN and ANK via hydrogen bond network (Figure 4C and D). It indicates that R240 methylation dramatically decreased interactions between R240 and H236. It further weakened the stability of the closed state of SHANK2. Thus, structural analyses suggest that SHANK2 R240 methylation disrupted SPN-ANK domain blockade to ‘open’ SHANK2, providing more chances for insertion of partner proteins.

SHANK2 R240 methylation recruits FAK/dynamin2/talin complex to endosome A previous study reported that SHANK3 SPN domain interacts with the ANK domain in an intramo- lecular manner, thereby restricting access of either Sharpin or a-fodrin (Mameza et al., 2013). To further figure out which SHANK2-bound proteins might be affected by SHANK2 R240 methylation induced structural changes, we used mass spectrometry to find the possible regulatory factors. The mass spectrometric data showed that SHANK2 could interact with numerous endosome associate proteins, including b1-integrin, talin, FAK, EEA1, dynamin2, clathrin, AP2 and cortactin (Figure 5A,B and Figure 5—figure supplement 1A), suggesting that methylated SHANK2 might contribute to endosome formation. To test this hypothesis, we first verified the mass spec data by using CoIP assays and we confirmed that talin, FAK, dynamin2, cortactin and SHANK2 were in the same complex in MDA-MB-231 cells (Figure 5C). To determine whether PRMT7-mediated SHANK2 methylation is involved in regulation of endocytosis, we overexpressed PRMT7 in MCF7 cells (low level of PRMT7). We found that overexpression of PRMT7 promoted the co-precipitation of dynamin2/talin/ FAK/SHANK2 with cortactin in MCF7 cells, and the interaction was reduced in PRMT7 depleted MDA-MB-231 cells (Figure 5D and F). Meanwhile, the PRMT7 enzymatic activity mutation (PRMT7 Mut) and PRMT7 R531 mutant attenuated the formation of dynamin2/talin/FAK/SHANK2/cortactin complex in PRMT7 depleted MDA-MB-231 cells (Figure 5—figure supplement 1B and C). Addition- ally, overexpression of PRMT7 triggered an accumulation in the number of EEA1-positive endosomes with more talin, FAK, EEA1 and dynamin2 colocalization in MCF7 cells, and the colocalization was attenuated in PRMT7 depleted MDA-MB-231 cells (Figure 5E and G). Consistently, the formation of dynamin2/talin/FAK/SHANK2/cortactin was significantly increased by reconstituted expression of SHANK2 WT but not of SHANK2 R240K in SHANK2 depleted MDA-MB-231 cells (Figure 5H). Meanwhile, SHANK2 WT promoted the recruitment of EEA1-positive endosomes and the majority of SHANK2 was associated with endosome associate proteins, which was significantly reduced by SHANK2 R240K in MDA-MB-231 and BT549 cells (Figure 5I and Figure 5—figure supplement 1D). Consistent with this finding, the interaction of dynamin2/talin/FAK/SHANK2/cortactin and the localization between talin, FAK, EEA1 and dynamin2 with endosome compartment was enhanced by reconstituted expression of SHANK2 R240F (as a methyl-mimic) but not of SHANK2 WT or SHANK2 R240K in MCF10A cells expressing low level of PRMT7 (Figure 5J and K). To assess the requirement of SHANK2 in PRMT7-induced interaction between talin and FAK, we silenced SHANK2 by shRNA in PRMT7-MCF7 cells. SHANK2 silencing partially reduced the formation of dynamin2/talin/FAK/SHANK2/cortactin complex (Figure 5—figure supplement 2A) and markedly decreased the interaction between talin and FAK (Figure 5—figure supplement 2B). Together, our data suggest that SHANK2 R240 di-methylation catalysed by PRMT7 is in favour of the assembly of a multi-protein complex to facilitate endosome formation.

SHANK2 R240 methylation activates endosomal FAK signalling Persistent activation of FAK signalling on endosomes promotes cancer cell dissemination (Alanko and Ivaska, 2016). To determine whether SHANK2 methylation was involved in endosomal FAK pathway activation, we examined phosphorylation of FAK and its downstream cortactin signalling cascade. As expected, overexpression of PRMT7 markedly increased FAK and cortactin

Liu et al. eLife 2020;9:e57617. DOI: https://doi.org/10.7554/eLife.57617 8 of 27 This article has been retracted. Read the retraction notice Research article Cancer Biology Cell Biology

Figure 5. SHANK2 R240 methylation promotes FAK/dynamin2/talin complex co-localized with endosome. (A) SHANK2 associated proteins from HA- SHANK2 expressing stable MDA-MB-231 cells were immunopurified with anti-HA (a-HA) affinity resins. The protein bands were analyzed by mass spectrometry. (B) Representative peptide fragments of SHANK2 associated proteins and peptide coverage of the indicated proteins are shown. (C) Endogenous talin, FAK, dynamin2, EEA1 and SHANK2 were IP from MDA-MB-231 cells, with indicated antibodies, and the binding of talin, FAK, dynamin2 and SHANK2 was examined by western blot. (D) MCF7 cells with expression of the indicated Flag-Vector or Flag-tagged PRMT7. Immunoprecipitation of cortactin with anti-cortactin antibody was performed. (E) Confocal images of PRMT7, dynamin2, SHANK2, EEA1, talin, Rab5, FAK, cortactin and DAPI staining in MCF7 cells with expression of the indicated Flag-Vector or Flag-tagged PRMT7. Scale bars, 10 mm. (F) MDA-MB- 231cells with or without stable expression of the indicated PRMT7 shRNA or a control shRNA. Immunoprecipitation of cortactin with anti-cortactin antibody was performed. (G) confocal images of PRMT7, dynamin2, SHANK2, EEA1, talin, Rab5, FAK, cortactin and DAPI staining in MDA-MB-231cells with or without stable expression of the indicated PRMT7 shRNA or a control shRNA. Scale bars, 10 mm. (H) MDA-MB-231cells expressing SHANK2 shRNA with or without reconstituted expression of WT SHANK2 or SHANK2 R240K mutant. Immunoprecipitation of cortactin with anti-cortactin antibody was performed. (I) Confocal images of PRMT7, dynamin2, SHANK2, EEA1, talin, Rab5, FAK, cortactin and DAPI staining in MDA-MB-231cells expressing SHANK2 shRNA with or without reconstituted expression of WT SHANK2 or SHANK2 R240K mutant. Scale bars, 10 mm. (J) MCF10A cells with reconstituted expression of SHANK2 WT, SHANK2 R240K or SHANK2 R240F (arginine to phenylalanine) mutant. Immunoprecipitation of SHANK2 with anti-SHANK2 antibody was performed. (K) Confocal images of PRMT7, dynamin2, SHANK2, EEA1, talin, Rab5, FAK, cortactin in MCF10A cells with reconstituted expression of SHANK2 WT, SHANK2 R240K or SHANK2 R240F mutant. Scale bars, 10 mm. The online version of this article includes the following figure supplement(s) for figure 5: Figure supplement 1. SHANK2 was essential for the interaction and activity between talin and FAK. Figure supplement 2. SHANK2 was necessary for the interaction between talin and FAK. Figure 5 continued on next page

Liu et al. eLife 2020;9:e57617. DOI: https://doi.org/10.7554/eLife.57617 9 of 27 This article has been retracted. Read the retraction notice Research article Cancer Biology Cell Biology

Figure 5 continued Figure supplement 3. SHANK2 was co-localized with exosome markers.

phosphorylation in MCF7 cells, and PRMT7 depletion profoundly decreased FAK and cortactin phosphorylation in MDA-MB-231 cells (Figure 6A and B). Consistently, FAK and cortactin were activated by reconstituted expression of SHANK2 WT but not of SHANK2 R240K (Figure 6C). Furthermore, blocking FAK activation with FAK inhibitor GSK2256098 did inhibit phosphorylation of FAK and

Figure 6. SHANK2 R240 methylation activated endosomal FAK signals. (A) Phosphorylated/total FAK and cortactin were determined in MCF-7 cells expressing the indicated Flag-tagged PRMT7. Western blot was performed with the indicated antibodies. (B) Phosphorylated/total FAK and cortactin were determined in MDA-MB-231 cells with or without stable expression of the indicated SHANK2 shRNA or a control shRNA. Western blot was performed with the indicated antibodies. (C) Phosphorylated/total FAK and cortactin were determined in MDA-MB-231 cells with or without expressing SHANK2 shRNA and with or without reconstituted expression of WT SHANK2 or SHANK2 R240K mutant. Western blot was performed with the indicated antibodies. (D) Phosphorylated/total FAK and cortactin were determined in MDA-MB-231 cells expressing SHANK2 shRNA with or without reconstituted expression of WT SHANK2 or SHANK2 R240K or SHANK2 R240F mutant, SHANK2 R240F were treated with GSK2256098 (10 mM) or DMSO as control. Western blot was performed with the indicated antibodies. (E) Phosphorylated/total FAK and cortactin were determined in MCF10A cells co-transfected with SHANK2 and/or FAK plasmids. Western blot was performed with the indicated antibodies. (F) Phosphorylated/total FAK and cortactin were determined in MDA-MB-231 cells expressing SHANK2 shRNA with or without reconstituted expression of WT SHANK2, SHANK2 R240K or SHANK2 R240F mutant. SHANK2 R240F group was treated with dynasore (80 mM) or DMSO as control. Western blot was performed with the indicated antibodies. (G) Phosphorylated/total FAK and cortactin were determined in MDA-MB-231 cells expressing SHANK2 shRNA with or without reconstituted expression of WT SHANK2, SHANK2 R240K or SHANK2 R240F mutant. SHANK2 R240F with or without stable expression of the indicated EEA1 shRNA or a control shRNA. Western blot was performed with the indicated antibodies. The online version of this article includes the following figure supplement(s) for figure 6: Figure supplement 1. SHANK2 R240F activated FAK and cortactin.

Liu et al. eLife 2020;9:e57617. DOI: https://doi.org/10.7554/eLife.57617 10 of 27 This article has been retracted. Read the retraction notice Research article Cancer Biology Cell Biology cortactin upregulated by SHANK2 R240F in SHANK2 depleted MDA-MB-231 cells (Figure 6D). The similar results were also observed in MCF10A cells co-transfected with SHANK2 R240F and FAK WT, but not with SHANK2 WT or SHANK2 R240K and FAK Y397K (Figure 6E and Figure 6—figure supplement 1A–C). Consistently, we found that SHANK2 R240F or SHANK2 WT, but not SHANK2 R240K increased phosphorylation of FAK and cortactin in SHANK2 depleted MDA-MB-231 cells (Figure 6F). To determine if PRMT7-dependent SHANK2 methylation responsible for FAK activation was dependent on endocytosis, MDA-MB-231-SHANK2 depletion cells with reconstituted expression of SHANK2 R240F were treated with the dynamin inhibitor-dynasore. Treatment with dynasore or silencing of EEA1 greatly decreased SHANK2 R240F induced-phosphorylation of FAK and cortactin in MDA-MB-231 cells (Figure 6F and G). FAK activation was also thought to inhibit apoptosis for cancer cell dissemination. We found that apoptotic cells were increased upon reconstituted expression of SHANK2 R240K but not of SHANK2 WT (Figure 6—figure supplement 1D). Collectively, these findings provide evidence that SHANK2 di-methylation mediated by PRMT7 potentiates FAK and cortactin activation through activating endocytosis.

SHANK2 R240 methylation promotes migration and invasion through activating endosomal signals Thus far, we have found that the PRMT7-mediated SHANK2 R240 methylation triggered breast cancer cell migration/invasion, and SHANK2 R240 methylation promoted endocytosis and endosomal FAK activation. We next wonder if the SHANK2 methylation-promoted migration and invasion is dependent on the activation of endosomal signals. Indeed, treatment with dynasore decreased PRMT7 induced-EMT program and migration/invasion capabilities of MCF7 cells (Figure 7A–C). Likewise, EMT and cell migration/invasion were activated by reconstituted expression of SHANK2 R240F or SHANK2 WT but not of SHANK2 R240K in SHANK2-depleted MDA-MB-231 cells (Figure 7D–F). To determine the functional role of SHANK2 R240 methylation is dependent on endocytosis, we treated SHANK2 R240F MDA-MB-231 cells with dynasore, and found that dynasore dramatically inhibited the effects of SHANK2 R240F induced-EMT and cell migration/invasion (Figure 7D–F). Since multiple endosomal signalling pathways are EEA1 dependent, we silenced EEA1 to test the impact of SHANK2 R240 methylation on EMT program and migration/invasion capabilities. Similarly, knockdown of EEA1 also markedly reduced SHANK2 R240F induced-EMT and cell migration/invasion (Figure 7G–I). Since SHANK2 R240 methylation promotes cell migration/invasion through activating endosomal FAK signalling, we treated SHANK2 R240F MDA-MB-231 cells with FAK inhibitor GSK2256098, and found that GSK2256098 also inhibited the effects of SHANK2 R240F induced-EMT and cell migration/invasion (Figure 7J–L). Taken together, these results indicate that the PRMT7-induced SHANK2 R240 methylation triggers breast cancer cell migration and invasion through activating endosomal FAK signalling.

SHANK2 R240 methylation promotes breast cancer metastasis through elevating endosomal FAK activation The above findings intrigued us to test the functions of SHANK2 R240 methylation in the pathological progression of breast cancer. To assess the biological effects of SHANK2 R240 methylation in vivo, we examined whether SHANK2 di-methylation affected tumour metastasis in xenograft mouse models. We injected equal amounts of MDA-MB-231-scramble cells, MDA-MB-231-SHANK2 depletion cells, MDA-MB-231-SHANK2 depletion cells with reconstituted expression of SHANK2 WT, SHANK2 R240K or SHANK2 R240F into the vail veins of female nude BALB/c nude mice, and mice bearing SHANK2 R240F were treated with or without FAK inhibitor GSK2256098. The results demonstrated that lung metastases and the number of metastatic pulmonary nodules were dramatically decreased by reconstituted expression of SHANK2 R240K, but not of SHANK2 WT or SHANK2 R240F (Figure 8A). We also discovered that the mice injected with SHANK2 R240F cells and treated with GSK2256098 formed fewer lung metastatic foci than that injected with SHANK2 R240F (Figure 8B). In addition, immunohistochemistry staining results indicated that SHANK2 R240F expression reinforced FAK Y397 and cortactin Y421 phosphorylation, whereas SHANK2 R240F with GSK2256098 treatment profoundly inhibited SHANK2 R240F induced-FAK Y397 and cortactin Y421 phosphorylation (Figure 8C and D). Our observations indicate that SHANK2 di-methylation induces metastasis of MDA-MB-231 cells in vivo through activating FAK signalling. Likewise, we analyzed 27

Liu et al. eLife 2020;9:e57617. DOI: https://doi.org/10.7554/eLife.57617 11 of 27 This article has been retracted. Read the retraction notice Research article Cancer Biology Cell Biology

Figure 7. SHANK2 R240 methylation promoted migration and invasion of breast cancer cells by activating endosomal FAK signals. (A) MCF7cells expressing the indicated Flag-tagged PRMT7. MCF7-Vector and MCF7-PRMT7 groups were treated with dynasore (80 mM) or DMSO as control. Western blot was performed with the indicated EMT marker antibodies. (B and C) MCF7 cells expressing the indicated Flag-tagged PRMT7. MCF7- Vector and MCF7-PRMT7 groups were treated with dynasore (80 mM) or DMSO as control. Cell migration (B) and Invasion (C) were determined by Figure 7 continued on next page

Liu et al. eLife 2020;9:e57617. DOI: https://doi.org/10.7554/eLife.57617 12 of 27 This article has been retracted. Read the retraction notice Research article Cancer Biology Cell Biology

Figure 7 continued transwell assays. (n = 3, independent experiments). Scale bars: 50 mm. Data represent the mean ± SD of three independent experiments. Scale bars,100 mm. ***p<0.001, Student’s t test. (D) MDA-MB-231 cells expressing SHANK2 shRNA with or without reconstituted expression of WT SHANK2, SHANK2 R240K or SHANK2 R240F mutant. SHANK2 R240F group was treated with dynasore (80 mM) or DMSO as control. Western blot was performed with the indicated EMT marker antibodies. (E and F) MDA-MB-231 cells expressing SHANK2 shRNA with or without reconstituted expression of WT SHANK2, SHANK2 R240K or SHANK2 R240F mutant. SHANK2 R240F group was treated with dynasore (80 mM) or DMSO as control. Cell migration (E) and Invasion (F) were determined by transwell assays. (n = 3, independent experiments). Scale bars: 100 mm. ***p<0.001, Student’s t test. (G) MDA-MB-231 cells expressing SHANK2 shRNA with or without reconstituted expression of WT SHANK2, SHANK2 R240K or SHANK2 R240F mutant. SHANK2 R240F with or without stable expression of the indicated EEA1 shRNA or a control shRNA. Western blot was performed with the indicated EMT marker antibodies. (H and I) MDA-MB-231 cells expressing SHANK2 shRNA with or without reconstituted expression of WT SHANK2, SHANK2 R240K or SHANK2 R240F mutant. SHANK2 R240F with or without stable expression of the indicated EEA1 shRNA or a control shRNA. Cell migration (H) and Invasion (I) were determined by transwell assays. (n = 3, independent experiments). Scale bars: 100 mm. ***p<0.001, Student’s t test. (J) MDA-MB-231 cells expressing SHANK2 shRNA with or without reconstituted expression of WT SHANK2, SHANK2 R240K or SHANK2 R240F mutant. SHANK2 R240F group was treated with GSK2256098 (10 mM) or DMSO as control. Western blot was performed with the indicated EMT marker antibodies.

human primary breast cancer specimens (Figure 3A and B) with PRMT7, p-FAK and p-cortactin antibody. Immunohistochemistry staining results revealed a correlation among PRMT7, FAK Y397 and cortactin Y421 phosphorylation levels, and the clinical aggressiveness of breast cancer (Figure 8E,F and Figure 8—figure supplement 1). Together, these data indicate that SHANK2 R240 methylation promotes breast cancer metastasis through activating FAK signalling.

Discussion Protein arginine methylation modification is involved in a variety of cellular biological events, such as epigenetic gene activation/repression, alternative mRNA splicing, DNA repair and immune surveil- lance (Jarrold and Davies, 2019). Recent reports showed that endocytosis activity required methionine and PRMT1 (Albrecht et al., 2018). Nevertheless, the roles and mechanisms of arginine methylation in regulation of cell endocytosis remain poorly defined. In this study, we report a new substrate of PRMT7, the scaffold protein SHANK2, which is di-methylated at arginine 240 residue to maintain endocytic activity. In particular, SHANK2 R240K methylation disturbs SPN-ANK domain blockade of SHANK2, thereby resulting in the accumulation of dynamin2, talin, FAK and cortactin on the endosome. SHANK2 R240 methylation further activates endosomal FAK/cortactin signals, which increases the migration of SHANK2-dependent breast cancer metastasis. (Figure 9). Cancer cells are highly compartmentalized by the endomembrane system, which is functionally defined by the scaffold proteins dynamin, EEA1 or APPL1 (Sandra, 2017). Our mass spectrometry results suggested that methylated SHANK2 not only interacted with talin, FAK and cortactin, but also with endosome associate proteins such as clatharin, AP-2 and dynamin2 (Figure 5B). It is implicated that the methylated SHANK2 might be involved in clatharin-mediated endocytosis. Dynamin is best known for its role in catalyzing membrane scission at late stages of clathrin-mediated endocytosis to release clathrin-coated vesicles into the cytosol (Kaksonen and Roux, 2018). Furthermore, increasing evidence suggests that dynamin can also regulate earlier stages of endosome maturation through binding the scaffold protein EEA1, in turn regulate the recruitment of other factors to the membrane that control endosomal sorting and maturation (Hamidi and Ivaska, 2018). Our results demonstrated that PRMT7 promoted dynamin2 interaction with methylated SHANK2 (Figure 5H). Moreover, the PRMT7-mediated SHANK2 methylation rendered EEA1 to co-localize with SHANK2 (Figure 5I). These results indicate that methylated SHANK2 might enhance the activity of dynamin2 and thus regulate the formation of endosome. Scaffold proteins SHANK1, 2, three are able to bind and interact with a wide range of proteins including actin binding proteins and actin modulators, such as dynamin2, cortactin, RICH2, and PIX (Lee et al., 2010; Sheng and Kim, 2000). SHANK1, 2, three have been reported to affect the structure and function of the neural circuits and to regulate autism spectrum disorders; but their roles in tumourigenesis are far from illuminated. Recent studies reported that SHANK1 and SHANK3 acted as negative regulators of integrin activity by binding R-Ras, thereby inhibiting migration and invasion of MDA-MB-231 cells (Lilja et al., 2017). In contrast to SHANK1 and SHANK3, the present study revealed that SHANK2, especially the methylated SHANK2, was correlated with high level of inci- dence of breast cancer (Figure 3B). Our data demonstrated that methylated SHANK2 promoted

Liu et al. eLife 2020;9:e57617. DOI: https://doi.org/10.7554/eLife.57617 13 of 27 This article has been retracted. Read the retraction notice Research article Cancer Biology Cell Biology

Figure 8. Arginine methylation at SHANK2 R240 promoted metastasis through activates FAK signalling. (A) Equal numbers of MDA-MB-231 cells expressing SHANK2 shRNA with or without reconstituted expression of WT SHANK2, SHANK2 R240K or SHANK2 R240F mutant. SHANK2 R240F group was treated with GSK2256098 or DMSO. Cells were tail-vein injected into BALB/c nude mice, and lung metastasis was determined. The gross appearance of the lungs and the tumour nodules on the lungs were examined. Tumours were paraffin embedded and stained with H and E at Day12. n = 5 tumours in each group. IHC analyses of tumour tissues were performed with anti-p-FAK or anti-p-cortactin antibody. Scale bars,100 mm. (B) The number of visible surface metastatic lesions in lungs was counted. (n = 5 mice for each group, **p<0.01, ***p<0.001, ns = not significant, one-way ANOVA test). (C, D) p-FAK and p-cortactin -positive cells were quantified in 10 microscope fields. **p<0.01, ***p<0.001, ns = not significant, one-way ANOVA test. (E, F) Typical pictures of the immunohistochemical staining of PRMT7, p-FAK and p-cortactin in breast cancer samples. Scale bars,100 mm. n = 27, **p<0.01, Student’s t test. The online version of this article includes the following figure supplement(s) for figure 8: Figure supplement 1. PRMT7 was associated with III stage breast cancer.

breast cancer metastasis (Figure 8A). Like SHANK3, our mass spectrometry results demonstrated that methylated SHANK2 could bind to receptor proteins, not only integrin but also Met, NRP1 and EGFR, which indicated that PRMT7-SHANK2 might be involved in receptor mediated endocytosis (Figure 5—figure supplement 1A). Although several studies reported that SHANK2 and SHANK3 could form heterodimers, our mass spectrometry results did not found SHANK1 or SHANK3

Liu et al. eLife 2020;9:e57617. DOI: https://doi.org/10.7554/eLife.57617 14 of 27 This article has been retracted. Read the retraction notice Research article Cancer Biology Cell Biology

Figure 9. A model for PRMT7-mediated SHANK2 methylation that promotes breast cancer migration through activating endosomal FAK signalling In the absence of PRMT7, SHANK2 cannot interact with dynamin2/talin/FAK/cortactin complex to endosome. In the presence of PRMT7, R240-methylated SHANK2 disturbs SPN-ANK domain blockade of SHANK2, thereby promoting the co-localization of dynamin2/talin/FAK/cortactin complex on endosome, further activating FAK signalling to promote tumour cells migration.

interacting with SHANK2. Moreover, by comparing SHANK3 protein sequence with SHANK2, we did not find the conservative RXR motif that was a potential methylation sequence by PRMT7. Therefore, whether SHANK3 and SHANK2 have crosstalk still needs further study. The intracellular trafficking of endosome must be tightly controlled in space and time to enable effective cell adhesion and microenvironmental sensing and compartmentalize it from other cellular processes. Organelles of these intracellular trafficking pathways—including endosomes, lysosomes, exosome, the endoplasmic reticulum (ER), the Golgi apparatus, and the plasma membrane are cou- pled by clatharin-dependent membrane vesicles delivery. In our study, we also demonstrated that methylated SHANK2 could interact with relative endomembrane organelles marker, such as EEA1, LAMP1, Calnexin, GOLM1, Ninein, CD63, TOM70 and LanminA/C (Figure 5—figure supplement 1A). These results indicated that SHANK2 could localize not only on endosomes but also on lyso- some, mitochondria, ER, Golgi, centrosome, exosome and nuclear. Exosomes are key mediators of intercellular communication and can be detected in the tumour microenvironment. Although a small amount of the cell surface SHANK2 was detected, it was barely detected on plasma membrane by immunofluorescence analysis (Figure 5L). These data suggested that SHANK2 was rapidly internalized after recycling back to the cell surface and/or they might transport to the extracellular space by secreted exosomes. Exosomes are vesicles derived from late endosomes, also known as multivesicu- lar bodies, and can be secreted to the extracellular environments by most cell types. Indeed, we found that the methylated SHANK2 was co-localized with several common exosome marker proteins, including CD63 and CD81 (Figure 5—figure supplement 3A). Meanwhile, SHANK2 WT promoted recruitment of EEA1-positive endosomes and co-localized more CD63 and CD81 than that of SHANK2 R240K in MDA-MB-231 cells (Figure 5—figure supplement 3B). Thus, it is likely that the PRMT7-SHANK2 might be secreted by exosomes and continuously internalized and sustained the active talin/FAK/cortactin complexes on endosomes, and thereby provided persistent endosomal signals for tumour progression. In conclusion, data presented in this report outlines a working model in which PRMT7 regulates breast tumour metastasis by methylating SHANK2, a new substrate of PRMT7. Specifically, SHANK2

Liu et al. eLife 2020;9:e57617. DOI: https://doi.org/10.7554/eLife.57617 15 of 27 This article has been retracted. Read the retraction notice Research article Cancer Biology Cell Biology methylation enforces tumour metastasis, while it simultaneously promotes breast cancer cell migration and invasion via triggering endosomal FAK signal activation (Figure 9). As a key player in breast cancer development, methylated SHANK2 might be a potential therapeutic target.

Materials and methods Cell lines and reagents MCF10A, MCF7, T47D, BT474, MDA-MB-231, BT549 and HEK293T cell lines were purchased from ATCC, where all the cell lines were characterized by DNA finger printing and isozyme detection. Cells were immediately expanded and frozen such that they could be revived every 3 to 4 months. Cells were tested every 6 months to ensure negative for mycoplasma contamination with Lonza MycoAlert Mycoplasma Detection Kit (LT07-218, Lonza, Basel, Switzerland). All cell lines were mycoplasma negative. Cell lines were authenticated using Short Tandem Repeat (STR) analysis as described in 2012 in ANSI Standard (ASN-0002) by the ATCC Standards Development Organization (SDO). MCF10A cells were were cultured in DMEM/F12 supplemented with 20 ng/ml EGF (Sigma- Aldrich, E9644), 0.5 mg/ml hydrocortisone (Sangon, A610506), 100 ng/ml cholera toxin (Sigma- Aldrich, C8180), 10 mg/ml insulin (Gibco, Grand Island, NY, USA, 12585–014), hFGF basic (R and D Systems, Minneapolis, MN, USA, P09038), 10 U/ml penicillin-streptomycin, and 5% horse serum (Gibco), and incubated at 37˚C in 5% CO2. BT549, BT474 and T47D cells were cultured in RPMI- 1640 medium supplemented with 10% FBS (ExCell Bio). MDA-MB-231 cells were cultured in L15

medium with 10% FBS at 37˚C without CO2; HEK293T and MCF7 cells were cultured in DMEM containing 10% FBS. Dynasore (S8047), GSK591 (S8111), GSK2256098 (S5823) were purchased from Selleck Chemicals.

Antibodies and plasmids The following antibodies were used: antibodies against N-cadherin (561553, 1:1000 for WB, BD Bio- sciences), fibronectin (610077, 1:1000 for WB, BD Biosciences), b-catenin (610154, 1:1000 for WB, BD Biosciences), EEA1 (610456, 1:100 for IF, BD Biosciences), Rab5 (610724, 1:100 for IF, BD Bio- sciences), b-actin (A5228, A1978, 1:5000 for WB, Sigma-Aldrich), HA (H9658, 1:1000 for WB and 1:200 for IP, Sigma-Aldrich), MMP2 (GTX-104577, 1:1000 for WB, GeneTex), MMP9 (40086, 1:1000 for WB, GeneTex), p-cortactin (BS4778, 1:100 for IHC, bioworld), p-cortactin (ab47768, 1:1000 for WB, Abcam), mono methyl Arginine (ab415, 1:500 for WB, Abcam), asymmetric dimethyl Arginine (ab412, 1:500 for WB, Abcam), Dyn2 (ab3457, 1:100 for IF and 1:1000 for WB, Abcam), Flag (m20008, 1:1000 for WB and 1:200 for IP, Abmart), p-FAK (700255, 1:200 for IHC, Invitrogen), PRMT7 (sc-376077, 1:200 for IHC, santa cruz), PRMT7 (14762S, 1:200 for IP, 1:100 for IF and 1:1000 for WB, cell signaling technology), SHANK2 (#12218, 1:100 for IF, 1:200 for IP and 1:500 for WB, cell signaling technology), p-FAK (#8556, 1:1000 for WB, cell signaling technology), FAK (#3285, 1:1000 for WB and 1:100 for IF, cell signaling technology), p-talin (#13589, 1:1000 for WB, cell signaling technology), talin (#4021, 1:1000 for WB and 1:100 for IF, cell signaling technology), ZO-1 (#5406S, 1:1000 for WB, cell signaling technology), symmetric dimethyl Arginine (SYM10, 1:500 for WB, Milli- pore), PRMT5 (2882018, 1:1000 for WB, Millipore), cortactin (05–180, 16–228, 1:1000 for WB and 1:100 for IF, Millipore). Flag-cortactin expression vector was a gift from Dr. Alpha S. Yap (Division of Cell Biology and Molecular Medicine, The University of Queensland, Australia), HA-SHANK2 expression vector was a gift from Dr. Min Goo Lee (Department of Pharmacology, Pusan National University, Pusan, Korea), pcDNA3-HA-SHANK2, pWPXLD-SHANK2, pWPXLD-Flag-PRMT7, pWPXLD-Flag-PRMT5, pWPXLD- PRMT5. Additionally, shSHANK2#1 and shSHANK2#2 oligonucleotides were designed and cloned into lentiviral RNAi system pLKO.1. The sequences of shRNAs, which were designed to target human genes, were described below. shPRMT7#1: GGAACAAGCTATTTCCCATCC (targeting CDS region). shPRMT7#2: GGATGCAGTGTGTGTACTTCC (targeting CDS region). shSHANK2#1: GGAGTTAGTCAAAGCACAAAG (targeting CDS region). shSHANK2#2: GCTTGGAGCAAGAGAGAATTT (targeting 3’UTR region). shEEA1#1: GCGGAGTTTAAGCAGCTACAA (targeting CDS region).

Liu et al. eLife 2020;9:e57617. DOI: https://doi.org/10.7554/eLife.57617 16 of 27 This article has been retracted. Read the retraction notice Research article Cancer Biology Cell Biology Western blotting and immunoprecipitation Immunoprecipitation was performed with the lysates from indicated cultured cells and followed by the immunoblotting with corresponding antibodies. Briefly, the cells were collected and washed three times with cold PBS. Cells were harvested and lysed in buffer A [20 mM Tris-HCl (pH 8.0), 10 mM NaCl, 1 mM EDTA, and 0.5% NP-40] plus a protease inhibitor and phosphatase inhibitor cock- tails (Roche Diagnostics, Indianapolis, IN, USA) for 30 min at 4˚C. The supernatant was subjected to SDSPAGE, transferred to PVDF (EMD-Millipore) and detected by ECL reagents (GE Healthcare, Buckinghamshire, United Kingdom).

RNA extraction, reverse transcription and real-time RT-PCR Total RNA was extracted using Trizol reagent (TaKaRa, Dalian, China), according to the manufacturer’s instructions. RT-PCR was performed using the Access RT-PCR System from Promega. Real- time PCR was done using SYBR Green Realtime PCR Master Mix (TOYOBO, Osaka, Japan) on a LightCycler 480 Real Time PCR system (Roche).

The b-actin was used as an internal control. The sequences of the primers used in this study are described below b-actin: 5’-GAGCACAGAGCCTCGCCTTT-3’ and 5’-ATCCTTCTGACCCATGCCCA-3’. SHANK2: 5’- CGGGTAATCCTCCCAAATCA-3’ and 5’-CTTTATCCCGGCGTTTCATC-3’.

Lentiviral production and infection The lentivirus packaging vectors used were psPAX2 (Addgene, Cambridge, MA, USA) and pMD2.G (Addgene). Generation of lentivirus in HEK-293T cells and transfection of lentiviral constructs into recipient cell lines were performed according to the manufacturer’s instructions (Thermo Fisher Sci- entific, Carlsbad, CA, USA). Transfection reagent polyethylenimine (PEI) was purchased from Sigma- Aldrich.

Transwell migration and invasion assays Migration and invasion were evaluated by plating 2.5 Â 104 cells in the upper chambers of 8.0 mm pore size reduced growth factor Matrigel chambers or control non-coated chambers (BD Bioscien- ces) in 0.5% FBS/DMEM. Cells were allowed to invade for 24 hr towards DMEM/10% fixed with ice- cold methanol, and stained with 0.5% crystal violet. Two chambers per condition in three independent experiments were imaged at 5x and four fields per chamber were counted and analyzed.

Immunofluorescence staining The cells were washed three times with PBS and were fixed for 15 min at room temperature with 4% (vol/vol) paraformaldehyde and permeabilized with 0.2% Triton X-100 for 20 min on ice. Following permeabilization, nonspecific binding in the cells was blocked by incubation for 30 min at room temperature with 5% BSA in PBS and cells were incubated for 2 hr with specific primary antibodies (identified above, antibodies indicated in figures). After three washes with PBS, the cells were incubated for another 1 hr with secondary antibodies Alexa Fluor 488–conjugated anti–mouse IgG (A21202), Alexa Fluor 488–conjugated anti–rabbit IgG (A21206) or Alexa Fluor 555–conjugated anti–mouse IgG (A31570) (all from Invitrogen). Nuclei were counterstained with DAPI (4, 6-diamidino- 2-phenylin- dole; Sigma-Aldrich). All images were collected with a confocal microscope (Zeiss LSM 780).

Glutathione S-transferase pull-down assay Briefly, GST, GST-PRMT7 protein expressions were induced by adding 0.1 mmol/L IPTG at 25˚C for 8 hr with shaking, and then purified on glutathione-Sepharose4B according to the manufacturer’s instructions (GE Healthcare).

Affinity purification of Flag-tagged proteins HEK293T cells were transfected with pWPXLD-3xflag-PRMT7 plasmid, using the PEI reagent according to the manufacturer’s instructions. After transfection for 48 hr, cells were harvested and lysed in the buffer A containing protease inhibitor cocktail tablet (Roche). Total cell extracts were incubated with anti-Flag affinity gel (Biotool, Kirchberg, Switzerland) for 3 hr at 4˚C, and the

Liu et al. eLife 2020;9:e57617. DOI: https://doi.org/10.7554/eLife.57617 17 of 27 This article has been retracted. Read the retraction notice Research article Cancer Biology Cell Biology immunoprecipitates were washed 3 times with 13 Tris-buffered saline buffer [50 mM Tris-HCl (pH 7.4) and 150 mM NaCl]. Finally, the bound proteins were eluted with 3xflag peptide (ApexBio, Hous- ton, TX, USA) for 1 hr at 4˚C.

In vitro SHANK2 methylation assay HA-SHANK2 (5 mg) was incubated with GST-PRMT7 in the presence of S-adenosyl-methionine (SAM; 15 Ci/mmoL; PerkinElmer, Waltham, MA, USA) at 30˚C for 1 hr. The reaction was stopped by adding loading buffer followed by SDS PAGE.

Structure analysis The SHANK2 (NP_036441.2) structure was homology modelled via SWISS-MODEL web server based on the template of PDB ID 5G4X with the identity of 69%. The wild type SHANK2 model and the mutant one (Arg240Lys) were solvated in ~32,000 TIP3P water molecules with 150 mM NaCl in a 116 Â 116 Â 80 A˚ box. Both systems were built and pre-equilibrated with the CHARMM program using the CHARMM36 force field. The systems were equilibrated for 25ns using the NAMD2.12 program package under the periodic orthorhombic boundary conditions applied in all directions with the time step of 2 fs. The NPT ensemble was used for both simulations with pressure set to one atm and temperature to 310.15 K. Long-range electrostatic interactions were treated by the particle mesh Ewald (PME) algorithm. Non-bonded interactions were switched off at 10–12 A˚ .

MS analysis Flag-PRMT7 protein was purified from Flag-PRMT7- MDA-MB-231 cells and was then resolved by 10% SDS-PAGE. After Coomassie brilliant blue staining, the band corresponding to Flag-PRMT7 was excised for liquid chromatography-tandem mass spectrometry (LC–MS/MS) analysis performed in the Institute of Biophysics (Chinese Academy of Sciences, Beijing, China). HA-SHANK2 protein was purified from HA-SHANK2-MDA-MB-231 cells and was then resolved by 10% SDS-PAGE. After Coomassie brilliant blue staining, the band corresponding to HA-SHANK2 was excised for liquid chromatography-tandem mass spectrometry (LC–MS/MS) analysis performed in the Institute of Biophysics (Chinese Academy of Sciences, Beijing, China).

Breast cancer specimen collection Human breast tumour specimens were obtained from the Second Hospital of Jilin University, China. All the breast cancer tissue samples were collected from 27 patients enrolled on pathology department of the Second Hospital of Jilin University. All the samples were diagnosed by the pathology department of the Second Hospital of Jilin University to determine the stage and subtype of the breast tumour (Supplementary file 1 and Supplementary file 2). This experiment is an immunohistochemical study, no informed consent was needed due to the use of post-diagnostic left-over material. Ethical approval was obtained from the Ethics Review Committee of the Second Hospital of Jilin University (2019–107).

TCGA data analysis The Cancer Genome Atlas (TCGA) Breast cancer (BRCA) dataset was retrieved from http://cancerge- nome.nih.gov. Samples with clinical information and mRNA expression data were selected (1075 samples data) to evaluate the correlation between PRMT7 and the pathological stage of breast cancer patients.

Histologic evaluation and immunohistochemical staining The IHC staining was performed using a VECTASTAIN ABC kit according to the manufacturer’s instructions. Sections of patients with breast cancer were stained with antibodies against PRMT7, p-FAK or p-cortactin. The following proportion scores were assigned: 0, 1, 2, 3 and 4 if 0%, 0–10%, 11–50%, 51–75%, and 76–100% of the tumour cells exhibited positive staining, respectively. Also, the staining intensity was rated on a scale of 0 to 3: 0, negative; 1, weak; 2, moderate; and 3, strong. The proportion and intensity scores were then multiplied to obtain a total score.

Liu et al. eLife 2020;9:e57617. DOI: https://doi.org/10.7554/eLife.57617 18 of 27 This article has been retracted. Read the retraction notice Research article Cancer Biology Cell Biology Animal studies MDA-MB-231-shSHANK2-Vector, MDA-MB-231-shSHANK2 with SHANK2 WT or SHANK2 R240K (2 Â 106) cells were injected into tail-vein of 5-week-old female BALB/c nude mice. Following tumour cell injection, the mice were randomized (n = 5 mice per group) according to the following groups: 1 100 mL of a vehicle control (oral, daily; 2) 75 mg/kg GSK2256098 in 100 mL of vehicle (oral, daily); Therapy was initiated 10–14 days after tumour injection. Six weeks later, the mice were sacrificed and lungs fixed in formalin before embedded in paraffin using the routine procedure. Hematoxylin and eosin (H and E) staining was performed on sections from paraffin-embedded tissues. All the mice were housed in specific-pathogen free (SPF) conditions. All animal works were conducted in accordance with the IACUC guidelines and with the protocol approved by the IACUC of Northeast Normal University, reference assurance number AP2013011.

Statistical analysis Statistical analyses were performed using GraphPad Prism five software. Statistical parameters and methods are reported in the Figures and the Figure Legends. Unless specified, comparisons between groups were made by unpaired two-tailed Student’s t-test. A value of p<0.05 was considered statistically significant. For the correlation between PRMT7 expression and stage of breast cancer patients, a chi2 test was used, and the differences were considered as significance at p<0.05. A simultaneous comparison of more than two groups was conducted using one-way ANOVA (SPSS statistical package, version 12; SPSS Inc). Values of p<0.05 were considered statistically significant.

Acknowledgements We thank Dr. Min Goo Lee (Department of Pharmacology, Pusan National University, Pusan, Korea) for his generous gift of HA-SHANK2 expression plasmids, Dr. Alpha S Yap (The University of Queensland, St. Lucia, Brisbane, Australia) for providing Flag-cortactin expression plasmids. This work was supported by the grants from the National Natural Science Foundation of China (grant numbers: 31870765, 31571317, 31570718, 31771335, 31770825 and 21807098) and the Natural Sci- ence Foundation of Jilin Province (grant numbers: 20180101232JC, 20180101234JC and 20200404106YY).

Additional information

Funding Funder Grant reference number Author National Natural Science 31870765 Baiqu Huang Foundation of China National Natural Science 31571317 Jun Lu Foundation of China National Natural Science 31570718 Baiqu Huang Foundation of China National Natural Science 31771335 Yu Zhang Foundation of China National Natural Science 31770825 Jun Lu Foundation of China National Natural Science 21807098 Yibo Wang Foundation of China Natural Science Foundation of 20180101232JC Jun Lu Jilin Province Natural Science Foundation of 20180101234JC Yu Zhang Jilin Province Natural Science Foundation of 20200404106YY Yu Zhang Jilin Province

Liu et al. eLife 2020;9:e57617. DOI: https://doi.org/10.7554/eLife.57617 19 of 27 This article has been retracted. Read the retraction notice Research article Cancer Biology Cell Biology

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

Author contributions Yingqi Liu, Conceptualization, Resources, Data curation, Software, Formal analysis, Validation, Inves- tigation, Visualization, Methodology, Writing - original draft, Project administration, Writing - review and editing; Lingling Li, Guannan Wang, Resources, Software, Formal analysis, Methodology; Xiaoq- ing Liu, Conceptualization, Resources, Data curation, Formal analysis, Methodology; Yibo Wang, Conceptualization, Resources, Software, Formal analysis, Visualization, Methodology; Lingxia Liu, Conceptualization, Resources, Software, Investigation; Lu Peng, Jiayuan Liu, Data curation, Method- ology; Lian Zhang, Resources, Formal analysis, Methodology; Hongyuan Li, Software, Investigation, Methodology; Dong-Xu Liu, Conceptualization, Project administration; Baiqu Huang, Jun Lu, Super- vision, Funding acquisition, Validation, Visualization, Project administration, Writing - review and editing; Yu Zhang, Conceptualization, Supervision, Funding acquisition, Validation, Investigation, Writing - review and editing

Author ORCIDs Yingqi Liu https://orcid.org/0000-0002-3934-0673 Yu Zhang https://orcid.org/0000-0002-3702-6541

Ethics Human subjects: Human breast tumour specimens were obtained from the Second Hospital of Jilin University, China. All the breast cancer tissue samples were collected from 27 patients enrolled on pathology department of the Second Hospital of Jilin University. All the samples were diagnosed by the pathology department of the Second Hospital of Jilin University to determine the stage and subtype of the breast tumour. This experiment is an immunohistochemical study, no informed consent was needed due to the use of post-diagnostic left-over material. Ethical approval was obtained from the Ethics Review Committee of the Second Hospital of Jilin University (2019-107). Animal experimentation: All animal works were conducted in accordance with the IACUC guidelines and with the protocol approved by the IACUC at the Northeast Normal University, reference assurance number AP2013011.

Decision letter and Author response Decision letter https://doi.org/10.7554/eLife.57617.sa1 Author response https://doi.org/10.7554/eLife.57617.sa2

Additional files Supplementary files . Supplementary file 1. Clinical breast cancer adjacent tissues. . Supplementary file 2. Clinical breast cancer tissues. . Transparent reporting form

Data availability PDB accession number for SHANK2 structure analyse is pdb5G4X. Analysis of SHANK2 gene expression in human tissues using the Human Protein Atlas data.

The following previously published dataset was used:

Database and Author(s) Year Dataset title Dataset URL Identifier Lilja J, 2019 The crystal structure of the SHANK3 https://www.rcsb.org/ RCSB Protein Data Zacharchenko T, N-terminus structure/5G4X Bank, 5G4X Georgiadou M, Jacquemet G,

Liu et al. eLife 2020;9:e57617. DOI: https://doi.org/10.7554/eLife.57617 20 of 27 This article has been retracted. Read the retraction notice Research article Cancer Biology Cell Biology

Franceschi N, Peuhu E, Hamidi H, Pouwels J, Martens V, Nia FH, Beifuss M, Boeckers T, Kreienkamp HJ, Barsukov IL, Ivaska J

References Alanko J, Mai A, Jacquemet G, Schauer K, Kaukonen R, Saari M, Goud B, Ivaska J. 2015. Integrin endosomal signalling suppresses anoikis. Nature Cell Biology 17:1412–1421. DOI: https://doi.org/10.1038/ncb3250, PMID: 26436690 Alanko J, Ivaska J. 2016. Endosomes: emerging platforms for Integrin-Mediated FAK signalling. Trends in Cell Biology 26:391–398. DOI: https://doi.org/10.1016/j.tcb.2016.02.001, PMID: 26944773 Albrecht LV, Ploper D, Tejeda-Mun˜ oz N, De Robertis EM. 2018. Arginine methylation is required for canonical wnt signaling and endolysosomal trafficking. PNAS 115:E5317–E5325. DOI: https://doi.org/10.1073/pnas. 1804091115, PMID: 29773710 Baldwin RM, Haghandish N, Daneshmand M, Amin S, Paris G, Falls TJ, Bell JC, Islam S, Coˆte´J. 2015. Protein arginine methyltransferase 7 promotes breast Cancer cell invasion through the induction of MMP9 expression. Oncotarget 6:3013–3032. DOI: https://doi.org/10.18632/oncotarget.3072, PMID: 25605249 Bedford MT, Clarke SG. 2009. Protein arginine methylation in mammals: who, what, and why. Molecular Cell 33: 1–13. DOI: https://doi.org/10.1016/j.molcel.2008.12.013, PMID: 19150423 Blanc RS, Richard S. 2017. Arginine methylation: the coming of age. Molecular Cell 65:8–24. DOI: https://doi. org/10.1016/j.molcel.2016.11.003, PMID: 28061334 Dhar SS, Lee SH, Kan PY, Voigt P, Ma L, Shi X, Reinberg D, Lee MG. 2012. Trans-tail regulation of MLL4- catalyzed H3K4 methylation by H4R3 symmetric dimethylation is mediated by a tandem PHD of MLL4. Genes & Development 26:2749–2762. DOI: https://doi.org/10.1101/gad.203356.112, PMID: 23249737 Eke I, Deuse Y, Hehlgans S, Gurtner K, Krause M, Baumann M, Shevchenko A, Sandfort V, Cordes N. 2012.

b1Integrin/FAK/cortactin signaling is essential for human head and neck Cancer resistance to radiotherapy. Journal of Clinical Investigation 122:1529–1540. DOI: https://doi.org/10.1172/JCI61350, PMID: 22378044 Fedoriw A, Rajapurkar SR, O’Brien S, Gerhart SV, Mitchell LH, Adams ND, Rioux N, Lingaraj T, Ribich SA, Pappalardi MB, Shah N, Laraio J, Liu Y, Butticello M, Carpenter CL, Creasy C, Korenchuk S, McCabe MT, McHugh CF, Nagarajan R, et al. 2019. Anti-tumor activity of the type I PRMT inhibitor, GSK3368715, synergizes with PRMT5 inhibition through MTAP loss. Cancer Cell 36:100–114. DOI: https://doi.org/10.1016/j.ccell.2019. 05.014, PMID: 31257072 Geng P, Zhang Y, Liu X, Zhang N, Liu Y, Liu X, Lin C, Yan X, Li Z, Wang G, Li Y, Tan J, Liu DX, Huang B, Lu J. 2017. Automethylation of protein arginine methyltransferase 7 and its impact on breast Cancer progression. The FASEB Journal 31:2287–2300. DOI: https://doi.org/10.1096/fj.201601196R, PMID: 28188177 Grossfield A. 2020. WHAM: The Weighted Histogram Analysis Method. http://membrane.urmc.rochester.edu/ wordpress/?page_id=126 Haghandish N, Baldwin RM, Morettin A, Dawit HT, Adhikary H, Masson JY, Mazroui R, Trinkle-Mulcahy L, Coˆte´J. 2019. PRMT7 methylates eukaryotic translation initiation factor 2a and regulates its role in stress granule formation. Molecular Biology of the Cell 15:778–793. DOI: https://doi.org/10.1091/mbc.E18-05-0330 Hamidi H, Ivaska J. 2018. Every step of the way: integrins in Cancer progression and metastasis. Nature Reviews Cancer 18:533–548. DOI: https://doi.org/10.1038/s41568-018-0038-z, PMID: 30002479 Huang J, MacKerell AD. 2013. CHARMM36 all-atom additive protein force field: validation based on comparison to NMR data. Journal of Computational Chemistry 34:2135–2145. DOI: https://doi.org/10.1002/jcc.23354, PMID: 23832629 Jain K, Clarke SG. 2019. PRMT7 as a unique member of the protein arginine methyltransferase family: a review. Archives of Biochemistry and Biophysics 665:36–45. DOI: https://doi.org/10.1016/j.abb.2019.02.014, PMID: 30 802433 Jarrold J, Davies CC. 2019. PRMTs and arginine methylation: cancer’s Best-Kept Secret? Trends in Molecular Medicine 25:993–1009. DOI: https://doi.org/10.1016/j.molmed.2019.05.007 Jelinic P, Stehle JC, Shaw P. 2006. The testis-specific factor CTCFL cooperates with the protein methyltransferase PRMT7 in H19 imprinting control region methylation. PLOS Biology 4:e355. DOI: https://doi.org/10.1371/ journal.pbio.0040355, PMID: 17048991 Jeong HJ, Lee HJ, Vuong TA, Choi KS, Choi D, Koo SH, Cho SC, Cho H, Kang JS. 2016. Prmt7 deficiency causes reduced skeletal muscle oxidative metabolism and Age-Related obesity. Diabetes 65:1868–1882. DOI: https:// doi.org/10.2337/db15-1500, PMID: 27207521 Jeong HJ, Lee SJ, Lee HJ, Kim HB, Anh Vuong T, Cho H, Bae GU, Kang JS. 2020. Prmt7 promotes myoblast differentiation via methylation of p38MAPK on arginine residue 70. Cell Death & Differentiation 27:573–586. DOI: https://doi.org/10.1038/s41418-019-0373-y, PMID: 31243342 Kaksonen M, Roux A. 2018. Mechanisms of clathrin-mediated endocytosis. Nature Reviews. Molecular Cell Biology 19:313–326. DOI: https://doi.org/10.1038/nrm.2017.132, PMID: 29410531

Liu et al. eLife 2020;9:e57617. DOI: https://doi.org/10.7554/eLife.57617 21 of 27 This article has been retracted. Read the retraction notice Research article Cancer Biology Cell Biology

Karkhanis V, Wang L, Tae S, Hu YJ, Imbalzano AN, Sif S. 2012. Protein arginine methyltransferase 7 regulates cellular response to DNA damage by methylating promoter histones H2A and H4 of the polymerase d catalytic subunit gene, POLD1. Journal of Biological Chemistry 287:29801–29814. DOI: https://doi.org/10.1074/jbc. M112.378281, PMID: 22761421 Kumar S, Rosenberg JM, Bouzida D, Swendsen RH, Kollman PA. 1992. THE weighted histogram analysis method for free-energy calculations on biomolecules. I. the method. Journal of Computational Chemistry 13:1011– 1021. DOI: https://doi.org/10.1002/jcc.540130812 Lee JS, Lee YM, Kim JY, Park HW, Grinstein S, Orlowski J, Kim E, Kim KH, Lee MG. 2010. BetaPix up-regulates na+/H+ exchanger 3 through a Shank2-mediated protein-protein interaction. The Journal of Biological Chemistry 285:8104–8113. DOI: https://doi.org/10.1074/jbc.M109.055079, PMID: 20080968 Lilja J, Zacharchenko T, Georgiadou M, Jacquemet G, De Franceschi N, Peuhu E, Hamidi H, Pouwels J, Martens V, Nia FH, Beifuss M, Boeckers T, Kreienkamp HJ, Barsukov IL, Ivaska J. 2017. SHANK proteins limit integrin activation by directly interacting with Rap1 and R-Ras. Nature Cell Biology 19:292–305. DOI: https://doi.org/ 10.1038/ncb3487, PMID: 28263956 Lim S, Naisbitt S, Yoon J, Hwang JI, Suh PG, Sheng M, Kim E. 1999. Characterization of the shank family of synaptic proteins multiple genes, alternative splicing, and differential expression in brain and development. The Journal of Biological Chemistry 274:29510–29518. DOI: https://doi.org/10.1074/jbc.274.41.29510, PMID: 10506216 Mameza MG, Dvoretskova E, Bamann M, Ho¨ nck HH, Gu¨ ler T, Boeckers TM, Schoen M, Verpelli C, Sala C, Barsukov I, Dityatev A, Kreienkamp HJ. 2013. SHANK3 gene mutations associated with autism facilitate ligand binding to the Shank3 ankyrin repeat region. Journal of Biological Chemistry 288:26697–26708. DOI: https:// doi.org/10.1074/jbc.M112.424747, PMID: 23897824 McMahon HT, Boucrot E. 2011. Molecular mechanism and physiological functions of clathrin-mediated endocytosis. Nature Reviews Molecular Cell Biology 12:517–533. DOI: https://doi.org/10.1038/nrm3151, PMID: 21779028 Mei Y, Monteiro P, Zhou Y, Kim JA, Gao X, Fu Z, Feng G. 2016. Adult restoration of Shank3 expression rescues selective autistic-like phenotypes. Nature 530:481–484. DOI: https://doi.org/10.1038/nature16971, PMID: 26 886798 Monteiro P, Feng G. 2017. SHANK proteins: roles at the synapse and in autism spectrum disorder. Nature Reviews Neuroscience 18:147–157. DOI: https://doi.org/10.1038/nrn.2016.183, PMID: 28179641 Murphy DA, Courtneidge SA. 2011. The ’ins’ and ’outs’ of podosomes and invadopodia: characteristics, formation and function. Nature Reviews Molecular Cell Biology 12:413–426. DOI: https://doi.org/10.1038/ nrm3141, PMID: 21697900 Nader GP, Ezratty EJ, Gundersen GG. 2016. FAK, Talin and pipkig regulate endocytosed integrin activation to polarize focal adhesion assembly. Nature Cell Biology 18:491–503. DOI: https://doi.org/10.1038/ncb3333, PMID: 27043085 Naisbitt S, Kim E, Tu JC, Xiao B, Sala C, Valtschanoff J, Weinberg RJ, Worley PF, Sheng M. 1999. Shank, a novel family of postsynaptic density proteins that binds to the NMDA receptor/PSD-95/GKAP complex and cortactin. Neuron 23:569–582. DOI: https://doi.org/10.1016/S0896-6273(00)80809-0, PMID: 10433268 Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kale´L, Schulten K. 2005. Scalable molecular dynamics with NAMD. Journal of Computational Chemistry 26:1781–1802. DOI: https://doi. org/10.1002/jcc.20289, PMID: 16222654 Qin HD, Liao XY, Chen YB, Huang SY, Xue WQ, Li FF, Ge XS, Liu DQ, Cai Q, Long J, Li XZ, Hu YZ, Zhang SD, Zhang LJ, Lehrman B, Scott AF, Lin D, Zeng YX, Shugart YY, Jia WH. 2016. Genomic characterization of esophageal squamous cell carcinoma reveals critical genes underlying tumorigenesis and poor prognosis. The American Journal of Human Genetics 98:709–727. DOI: https://doi.org/10.1016/j.ajhg.2016.02.021, PMID: 27058444 Sala C, Pie¨ ch V, Wilson NR, Passafaro M, Liu G, Sheng M. 2001. Regulation of dendritic spine morphology and synaptic function by shank and homer. Neuron 31:115–130. DOI: https://doi.org/10.1016/S0896-6273(01) 00339-7, PMID: 11498055 Sandra LS. 2017. Reciprocal regulation of signaling and endocytosis: implications for the evolving Cancer cell. J Cell Biol. 216:2623–2632. DOI: https://doi.org/10.1083/jcb.201705017 Schmeisser MJ, Ey E, Wegener S, Bockmann J, Stempel AV, Kuebler A, Janssen AL, Udvardi PT, Shiban E, Spilker C, Balschun D, Skryabin BV, Dieck S, Smalla KH, Montag D, Leblond CS, Faure P, Torquet N, Le Sourd AM, Toro R, et al. 2012. Autistic-like behaviours and hyperactivity in mice lacking ProSAP1/Shank2. Nature 486:256–260. DOI: https://doi.org/10.1038/nature11015, PMID: 22699619 Schoenherr C, Frame MC, Byron A. 2018. Trafﬁcking of adhesion and growth factor receptors and their effector kinases. Annual Review of Cell and Developmental Biology 34:29–58. DOI: https://doi.org/10.1146/annurev- cellbio-100617-062559, PMID: 30110558 Scita G, Di Fiore PP. 2010. The endocytic matrix. Nature 463:464–473. DOI: https://doi.org/10.1038/ nature08910, PMID: 20110990 Sheng M, Kim E. 2000. The SHANK family of scaffold proteins. Journal of Cell Science 113:1851–1856. PMID: 10 806096 Tomar A, Lawson C, Ghassemian M, Schlaepfer DD. 2012. Cortactin as a target for FAK in the regulation of focal adhesion dynamics. PLOS ONE 7:e44041. DOI: https://doi.org/10.1371/journal.pone.0044041, PMID: 22952 866

Liu et al. eLife 2020;9:e57617. DOI: https://doi.org/10.7554/eLife.57617 22 of 27 This article has been retracted. Read the retraction notice Research article Cancer Biology Cell Biology

Trusolino L, Bertotti A, Comoglio PM. 2010. MET signalling: principles and functions in development, organ regeneration and Cancer. Nature Reviews. Molecular Cell Biology 11:834–848. DOI: https://doi.org/10.1038/ nrm3012, PMID: 21102609 Tu JC, Xiao B, Naisbitt S, Yuan JP, Petralia RS, Brakeman P, Doan A, Aakalu VK, Lanahan AA, Sheng M, Worley PF. 1999. Coupling of mGluR/Homer and PSD-95 complexes by the shank family of postsynaptic density proteins. Neuron 23:583–592. DOI: https://doi.org/10.1016/s0896-6273(00)80810-7, PMID: 10433269 Vanommeslaeghe K, Hatcher E, Acharya C, Kundu S, Zhong S, Shim J, Darian E, Guvench O, Lopes P, Vorobyov I, Mackerell AD. 2010. CHARMM general force field: a force field for Drug-Like molecules compatible with the CHARMM All-Atom additive biological force fields. Journal of Computational Chemistry 31:671–690. DOI: https://doi.org/10.1002/jcc.21367, PMID: 19575467 Verma N, Keinan O, Selitrennik M, Karn T, Filipits M, Lev S. 2015. PYK2 sustains endosomal-derived receptor signalling and enhances epithelial-to-mesenchymal transition. Nature Communications 6:6064. DOI: https://doi. org/10.1038/ncomms7064, PMID: 25648557 Vuong TA, Jeong HJ, Lee HJ, Kim BG, Leem YE, Cho H, Kang JS. 2020. PRMT7 methylates and suppresses GLI2 binding to SUFU thereby promoting its activation. Cell Death & Differentiation 27:15–28. DOI: https://doi.org/ 10.1038/s41418-019-0334-5, PMID: 31000813 Wang W, Liu Y, Liao K. 2011. Tyrosine phosphorylation of cortactin by the FAK-Src complex at focal adhesions regulates cell motility. BMC Cell Biology 12:49. DOI: https://doi.org/10.1186/1471-2121-12-49, PMID: 2207 8467 Wang Y, Guo J, Perissinotti LL, Lees-Miller J, Teng G, Durdagi S, Duff HJ, Noskov SY. 2016. Role of the pH in state-dependent blockade of hERG currents. Scientific Reports 6:32536. DOI: https://doi.org/10.1038/ srep32536, PMID: 27731415 Waterhouse A, Bertoni M, Bienert S, Studer G, Tauriello G, Gumienny R, Heer FT, de Beer TAP, Rempfer C, Bordoli L, Lepore R, Schwede T. 2018. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Research 46:W296–W303. DOI: https://doi.org/10.1093/nar/gky427, PMID: 297 88355 Won H, Lee HR, Gee HY, Mah W, Kim JI, Lee J, Ha S, Chung C, Jung ES, Cho YS, Park SG, Lee JS, Lee K, Kim D, Bae YC, Kaang BK, Lee MG, Kim E. 2012. Autistic-like social behaviour in Shank2-mutant mice improved by restoring NMDA receptor function. Nature 486:261–265. DOI: https://doi.org/10.1038/nature11208, PMID: 22699620 Xiuping H, Qing Y, Min C, Aimin L, Wenting M, Yuxin F, Yekaterina YZ, Kathleen LO, Craig WV, Side L, QingBai S. 2018. N-glycosylation-defective splice variants of neuropilin-1 promote metastasis by activating endosomal signals. Nature Communications 10:3708. DOI: https://doi.org/10.1038/s41467-019-11580-4 Yao R, Jiang H, Ma Y, Wang L, Wang L, Du J, Hou P, Gao Y, Zhao L, Wang G, Zhang Y, Liu DX, Huang B, Lu J. 2014. PRMT7 induces epithelial-to-mesenchymal transition and promotes metastasis in breast Cancer. Cancer Research 74:5656–5667. DOI: https://doi.org/10.1158/0008-5472.CAN-14-0800, PMID: 25136067 Yoon SY, Kwon SG, Kim YH, Yeo JH, Ko HG, Roh DH, Kaang BK, Beitz AJ, Lee JH, Oh SB. 2017. A critical role of spinal Shank2 proteins in NMDA-induced pain hypersensitivity. Molecular Pain 13:1744806916688902. DOI: https://doi.org/10.1177/1744806916688902, PMID: 28326932 Zhu F, Hummer G. 2012. Convergence and error estimation in free energy calculations using the weighted histogram analysis method. Journal of Computational Chemistry 33:453–465. DOI: https://doi.org/10.1002/jcc. 21989, PMID: 22109354

Liu et al. eLife 2020;9:e57617. DOI: https://doi.org/10.7554/eLife.57617 23 of 27 This article has been retracted. Read the retraction notice Research article Cancer Biology Cell Biology Appendix 1 Key resources table

Appendix 1—key resources table

Reagent type (species) or Source or resource Designation reference Identifiers Additional information Antibody Anti- N-cadherin BD Biosciences Cat# 561553, WB (1:1000) (Mouse monoclonal) RRID:AB_ 10713831 Antibody Anti- fibronectin BD Biosciences Cat# 610070, WB (1:1000) (Mouse monoclonal) RRID:AB_ 2105706 Antibody Anti-b-catenin BD Biosciences Cat# 610154 WB (1:1000) (Mouse monoclonal) Antibody Anti- EEA1 BD Biosciences Cat# 610456, IF (1:100) (Mouse monoclonal) RRID:AB_397829 Antibody Anti- Rab5 BD Biosciences Cat# 610724, IF (1:100) (Mouse polyclonal) RRID:AB_398047 Antibody Anti-b-actin Sigma-Aldrich Cat# A5228, WB (1:5000) (Mouse monoclonal) RRID:AB_262054 Antibody Anti- HA Sigma-Aldrich Cat# H9658, WB (1:1000) (Mouse monoclonal) RRID:AB_260092 IP (4 mg) Antibody Anti- MMP2 GeneTex Cat# GTX- WB (1:1000) (Rabbit polyclonal) 104577 RRID:AB_ 1950932 Antibody Anti-MMP9 GeneTex Cat# 40086 WB (1:1000) (Rabbit polyclonal) Antibody Anti- p-cortactin Bioworld Cat# BS4778, IHC (1:100) (Rabbit polyclonal) RRID:AB_ 1663129 Antibody Anti- p-cortactin Abcam Cat# ab47768, WB (1:1000) (Rabbit polyclonal) RRID:AB_869231 Antibody mono methyl Abcam Cat# ab415, WB (1:500) Arginine RRID:AB_304323 (Mouse monoclonal) Antibody asymmetric dimethyl Abcam Cat# ab412, WB (1:500) Arginine RRID:AB_304292 (Mouse monoclonal) Antibody Dyn2 Abcam Cat# ab3457, WB (1:1000) (Rabbit polyclonal) RRID:AB_ IF (1:100) 2093679 Antibody Flag Abmart Cat# M20008, WB (1:1000) (Mouse monoclonal) RRID:AB_ 2713960 Antibody p-FAK Invitrogen Cat# 700255, IHC (1:100) (Rabbit polyclonal) RRID:AB_ IP (4 mg) 2532307 Antibody PRMT7 santa cruz Cat# sc-376077, IHC (1:200) (Mouse monoclonal) RRID:AB_ 10990266 Antibody PRMT7 Cell Signaling Cat# 14762, WB (1:1000) (Rabbit monoclonal) Technology RRID:AB_ IP (4 mg) 2798599 IF (1:100)

Continued on next page

Liu et al. eLife 2020;9:e57617. DOI: https://doi.org/10.7554/eLife.57617 24 of 27 This article has been retracted. Read the retraction notice Research article Cancer Biology Cell Biology

Appendix 1—key resources table continued

Reagent type (species) or Source or resource Designation reference Identifiers Additional information Antibody SHANK2 Cell Signaling Cat# 12218, WB (1:500) (Rabbit polyclonal) Technology RRID:AB_ IP (4 mg) 2797848 IF (1:100) Antibody p-FAK Cell Signaling Cat# 8556, WB (1:1000) (Rabbit monoclonal) Technology RRID:AB_ 10891442 Antibody FAK Cell Signaling Cat# 3285, WB (1:1000) (Rabbit polyclonal) Technology RRID:AB_ IF (1:100) 2269034 Antibody p-talin Cell Signaling Cat# 13589, WB (1:1000) (Rabbit monoclonal) Technology RRID:AB_ 2798267 Antibody talin Cell Signaling Cat# 4021, WB (1:1000) (Rabbit monoclonal) Technology RRID:AB_ IF (1:100) 2204018 Antibody ZO-1 Cell Signaling Cat# 5406, WB (1:1000) (Rabbit polyclonal) Technology RRID:AB_ 1904187 Antibody symmetric dimethyl Millipore Cat# 07–412, WB (1:500) Arginine RRID:AB_ (Rabbit polyclonal) 11212396 Antibody PRMT5 Millipore Cat# 07–405, WB (1:1000) (Rabbit polyclonal) RRID:AB_310589 Antibody cortactin(Mouse Millipore Cat# 16–228, WB (1:1000) monoclonal) RRID:AB_441969 IF (1:100) Sequenced- Interference in the Addgene GGAACAAGCTATTTCCCATCC based reagent primer:PRMT7#1 Sequenced- Interference in the Addgene GGATGCAGTGTGTGTACTTCC based reagent primer:PRMT7#2 Sequenced- Interference in the Addgene GGAGTTAGTCAAAGCACAAAG based reagent primer:SHANK2#1 Sequenced- Interference in the Addgene GCTTGGAGCAAGAGAGAATTT based reagent primer:SHANK2#2 Sequenced- Interference in the Addgene GCGGAGTTTAAGCAGCTACAA based reagent primer:shEEA1#1 Sequenced- PCR Primer: Addgene PCR Primers GAGCACAGAGCCTCGCCTTT based reagent b-actin forward: Sequenced- PCR Primer: Addgene PCR Primers ATCCTTCTGACCCATGCCCA based reagent b-actin reverse: Sequenced- PCR Primer: Addgene PCR Primers CGGGTAATCCTCCCAAA based reagent SHANK2 forward: Sequenced- PCR Primer: Addgene PCR Primers CTTTATCCCGGCGTTTCATC based reagent SHANK2 reverse: Recombinant Flag-cortactin The lab of Dr. DNA reagent (plasmid) Alpha S. Yap.This paper Recombinant HA-SHANK2 The lab of Dr. Min DNA reagent (plasmid) Goo Lee.This paper Recombinant pcDNA3-HA- Addgene DNA reagent SHANK2 (plasmid)

Continued on next page

Liu et al. eLife 2020;9:e57617. DOI: https://doi.org/10.7554/eLife.57617 25 of 27 This article has been retracted. Read the retraction notice Research article Cancer Biology Cell Biology

Appendix 1—key resources table continued

Reagent type (species) or Source or resource Designation reference Identifiers Additional information Recombinant pWPXLD-SHANK2 Addgene DNA reagent (plasmid) Recombinant pWPXLD-Flag- Addgene DNA reagent PRMT7 (plasmid) Recombinant pWPXLD-PRMT7 Addgene DNA reagent (plasmid) Recombinant pWPXLD-Flag- Addgene DNA reagent PRMT5 (plasmid) Recombinant pWPXLD-PRMT5 Addgene DNA reagent (plasmid) Chemical Dynasore Selleck Cat# S8047 compound, drug Chemical GSK591 Selleck Cat# S8111 compound, drug Chemical GSK2256098 Selleck Cat# S5823 compound, drug Chemical EGF Sigma-Aldrich Cat# E9644 compound, drug Chemical hydrocortisone Sangon Cat# A610506 compound, drug Chemical cholera toxin Sigma-Aldrich Cat# C8180 compound, drug Chemical insulin Gibco, Grand Cat# 12585–014 compound, drug Island, NY, USA Chemical hFGF basic R and D Systems, Cat# P09038 compound, drug Minneapolis, MN, USA Strain, strain BALB/c nude Charles River Cat#CRL:194, background (CAnN.Cg-Foxn1nu/ Labs RRID:IMSR_CRL: Mus musculus Crl) 194 Cell line MCF10A (human; American Type Cat# CRL-10317, (Homo-sapiens) female) Culture RRID:CVCL_ Collection 0598 Cell line MCF7 (human; American Type Cat# HTB-22, (Homo-sapiens) female) Culture RRID:CVCL_ Collection 0031 Cell line T47D (human; American Type Cat# HTB-133, (Homo-sapiens) female) Culture RRID:CVCL_ Collection 0553 Cell line BT474(human; American Type Cat# HTB-20, (Homo-sapiens) female) Culture RRID:CVCL_ Collection 0179 Cell line MDA-MB-231 American Type Cat# HTB-26, (Homo-sapiens) (human; female) Culture RRID:CVCL_ Collection 0062 Cell line BT549(human; American Type Cat# HTB-122, (Homo-sapiens) female) Culture RRID:CVCL_ Collection 1092 Cell line HEK293T (human; American Type Cat# CRL-3216, (Homo-sapiens) fetus) Culture RRID:CVCL_ Collection 0063

Continued on next page

Liu et al. eLife 2020;9:e57617. DOI: https://doi.org/10.7554/eLife.57617 26 of 27 This article has been retracted. Read the retraction notice Research article Cancer Biology Cell Biology

Appendix 1—key resources table continued

Reagent type (species) or Source or resource Designation reference Identifiers Additional information Software, ImageJ Wayne Rasband, RRID:SCR_ algorithm National 003070 Institutes of Health Software, GraphPad Prism 8 GraphPad Version 8.3 algorithm Software RRID:SCR_ 002798

Liu et al. eLife 2020;9:e57617. DOI: https://doi.org/10.7554/eLife.57617 27 of 27