Upon developing cofactor-competitive PMT inhibitors (Wu et al., 2016; Zheng et al., 2012), we tailored the SAM analog sinefungin (Figure 1a) around its 6′-amino moiety to potentially engage CARM1’s substrate-binding pocket. 6′-homosinefungin (HSF, i.e., 1), a sinefungin analog with the insertion of 6′−methylene moiety, was discovered for its general high affinity to Type I PRMTs (Figure 1a,b, Figure 1—figure supplement 1, Supplementary file 1-Table A). As a SAM mimic, 1 binds to the Type I PRMTs (namely PRMT1, CARM1, PRMT6 and PRMT8) with IC₅₀ of 13‒300 nM (Figure 1a,c, Supplementary file 1-Table A). Its relative affinity to Type I PRMTs aligns with that of the SAM mimics SAH and SNF (around 20-fold lower IC₅₀ of 1 versus SAH and SNF, Figure 1a,c, Supplementary file 1-Table A). This observation argues that 1 retains the structural features of SAH and SNF to engage PRMTs and meanwhile leverages its 6′-methyleneamine group for additional interaction.

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To further explore the 6′-region of HSF, we synthesized HSF derivatives from the same precursor 3 (Figure 1b, Figure 1—figure supplement 2), by further expanding the 6′-methylene amine moiety with different substituents. The HSF derivative 2a (Figure 1b) was identified for its preferential binding to CARM1 with IC₅₀ = 30 ± 3 nM and >10 fold selectivity over other seven human PRMTs and 26 methyltransferases of other classes (Figure 1c, Supplementary file 1-Table A). The structural difference between 2a and 1 (Figure 1b) suggests that the N-benzyl substituent enables 2a to engage CARM1 through a distinct mechanism (see results below).

With 2a as a lead, we then explored its α-amino carboxylate moiety with different amides from the common precursor three and then the intermediate 4 (Figure 1—figure supplement 2), which led to the discovery of 5a. This engagement of CARM1 with 2a is expected to be largely maintained by 5a. Here, 5a shows an IC₅₀ of 43 ± 7 nM against CARM1 and a >10-fold selectivity over the panel of 33 diverse methyltransferases (Figure 1c, Supplementary file 1-Table A). In comparison, the negative control compounds 2b (Bn-SNF) (Zheng et al., 2012) and 5b (Figure 1b, Figure 1—figure supplement 3), which differ from 2a and 5a only by the 6′-methylene group, poorly inhibit CARM1 (IC₅₀ = 22 ± 1 µM and 1.91 ± 0.03 µM) (Figure 1c, Supplementary file 1-Table A). The dramatic increase of the potency of 2a and 5a in contrast to 2b and 5b supports an essential role of the 6′-methylene moiety upon binding CARM1. Distinguished from the SAM mimics SAH, SNF and 1 as nonspecific PMT inhibitors, 2a and 5a were developed as potent and selective SAM analogs.

With 2a and 5a characterized as CARM1 inhibitors, we leveraged orthogonal in vitro assays to explore their modes of interaction (Figure 2a). To examine whether 2a and 5a are SAM- or substrate-competitive, CARM1 inhibition by 2a and 5a was assessed in the presence of various concentrations of SAM cofactor and H3 peptide substrate (Figure 2b,c). IC₅₀ values of 2a and 5a showed a linear positive correlation with SAM concentrations, as expected for SAM-competitive inhibitors (Daigle et al., 2011; Luo, 2018; Zheng et al., 2012) .The K_d values of 2a and 5a (K_d,2a = 17 ± 8 nM; K_d,5a = 9 ± 5 nM) were extrapolated from the y-axis intercepts upon fitting the equation IC₅₀ = [SAM]×K_d/K_m,SAM+K_d (Figure 2b) (Segel, 1993). K_m,SAM of 0.21 ± 0.09 µM and 0.28 ± 0.14 µM (an averaged K_m,SAM = 0.25 µM) for competition with 2a and 5a, respectively, can also be derived through the ratio of the y-axis intercepts to the slopes (Figure 2b and Materials and methods) (Segel, 1993). By contrast, the presence of the H3 peptide substrate had negligible effect on the binding of 2a and 5a, indicating their substrate-noncompetitive character (Figure 2c). The SAM analogs 2a and 5a were thus characterized as SAM-competitive, substrate-noncompetitive inhibitors of CARM1.

Figure 2

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For the direct binding of 2a and 5a to CARM1, the CARM1-binding kinetics of 2a and 5a were examined using surface plasmon resonance (SPR) (Figure 2d). The SPR signal progression of 2a and 5a fits with a biphasic rather than a mono-phasic binding mode, with the lower K_i1,2a = 0.06 ± 0.02 µM, K_i1,5a = 0.10 ± 0.01 µM, and the higher K_i2,5b = 0.54 ± 0.07 µM, K_i2,2a = 0.4 ± 0.1 µM, probably because of the multi-phase binding kinetics of 2a and 5a (Figure 2d). To cross validate the binding of 2a and 5a to CARM1, we conducted an in vitro thermal shift assay, for which ligand binding is expected to increase CARM1’s thermal stability (Blum et al., 2014). The binding of 2a and 5a (at 5 μM concentration) increased the melting temperature (T_m) of CARM1 by 4.4°C and 6.5°C, respectively (Figure 2e, T_m, 2a = 44.2 ± 0.4 °C and T_m, 5a = 46.3 ± 0.3 °C versus T_m, DMSO = 39.8 ± 0.3 °C as control). By contrast, the binding of SAM and 1 show much reduced effects on T_m of CARM1 (Figure 2e, T_m, SAM = 40.1 ± 0.3 °C and T_m, 1 = 42.8 ± 0.4 °C versus T_m, DMSO = 39.8 ± 0.3 °C). Therefore, although the affinities of 1, 2a and 5a to CARM1 are comparable (IC₅₀ = 13‒43 nM, Figure 1c), their well-separated effects on T_m suggest that these inhibitors engage CARM1 differentially (see results below). The two orthogonal biochemical assays thus verified the tight binding of 2a and 5a with CARM1.

To further seek a structural rationale for 5a and 2a for CARM1 inhibition, we solved the X-ray structure of CARM1 in complex with 5a with resolution of 2.00 Å and modeled the CARM1 binding of 2a (Figure 3, Materials and methods). The overall topology of the CARM1–5a complex is indistinguishable with the V-shaped subunit of the CARM1 dimer in complex with SNF and 1 (details in the next section), which is typical of the Rossmann fold of Class I methyltransferases (Figure 3a,b, Table 1) (Luo, 2018). However, 5a adopts a noncanonical pose with its 6′-N-benzyl moiety in a binding pocket that used to be occupied by the α-amino carboxylate moiety of canonical ligands such as SAH, SNF and 1 (Figures 3c and 4), while the α-amino methoxyphenethyl amide moiety of 5a protrudes into the substrate-binding pocket (Boriack-Sjodin et al., 2016; Sack et al., 2011). This noncanonical mode is consistent with the SAM-competitive character of 5a (Figure 2b). In contrast to the noncanonical mode, Arg168 in the CARM1–5a complex adopts an alternative orientation (two possible configurations), accompanied by an altered conformation of Glu257, to accommodate the 6′-N-benzyl moiety of 5a (Figure 3d). The α-amino amide moiety of 5a also engages CARM1 through the combined outcomes of a hydrogen-bond network and hydrophobic interactions with nearby resides (Figure 3e). Interestingly, the overlaid structures of CARM1 in complex with 5a and a substrate peptide implicate a steric clash and thus a potential for binding competition between 5a and a CARM1 substrate (Figure 3f). However, the apparent substrate-noncompetitive character of 5a (Figure 2c) suggests that this steric clash might be avoided if there is no significant energy penalty when the substrate Arg adopts alternative conformation(s).

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The binding mode of the CARM1–2a complex was modeled via molecular docking followed by molecular dynamics (MD) simulation (Materials and methods). Here, we uncovered two distinct poses of 2a (Binding Pose 1/2 or BP1/2, Figure 3g, Figure 3—figure supplement 1). BP1 was characterized by the direct interaction between the α-amino carboxylate moiety of 2a and the guanidinium of Arg168, whereas BP2 features a titled orientation of Arg168 to accommodate the 6′-N-benzyl moiety of 2a (Figure 3g, Figure 3—figure supplement 1). The BP1 and BP2 of 2a closely resemble those of 1 and 5a, respectively, in terms of the orientations of Arg168 and the α-amino carboxylate moiety of the ligands. When the same modeling protocol was applied to the CARM1–SNF complex, only the canonical pose was identified (Materials and methods). Energy calculation indicated that both BP1 and BP2 are stable with comparable binding free energies. Interestingly, the side chain configurations of His414 in both BP1 and BP2 are different from those in the CARM1–5a complex and the CARM1–SNF complex (Figure 3g). Collectively, 5a and 2a, though structurally related to the SAM analogs 1 and SNF, engage CARM1 via distinct modes of interaction.

Upon comparing the CARM1 structure in complex with 5a and 2a, we observed the additional hydrogen-bond and hydrophobic interactions of 5a that involve its α-amino amide moiety (Figure 3e). Interestingly, these interactions do not increase but rather decrease the affinity of 5a to CARM1 by two-fold (K_d,2a = 17 ± 8 nM versus K_d,5a = 9 ± 5 nM, Figure 2b). By contrast, there is a significant 10-fold increase of affinity between 2b and 5b (Figure 1c, Supplementary file 1-Table A). These observations suggest that, although 5b facilitates CARM1’s engagement better than 2b via the former’s α-amino amide moiety, such an effect is dispensed with in the presence of the 6′-methylene (N-benzyl)amine moiety of 5a and 2a.

Given the tight CARM1 binding by 1, we solved the X-ray structure of CARM1 in complex with 1 (HSF) with a resolution of 2.00 Å (Figure 4). The overall folding of the CARM1–1 complex (PDB: 4IKP) is similar to those of 1 in complex with SNF and SAH (PDB: 2Y1X, 2Y1W) with a V-shape subunit in a dimer of dimers (Figure 4a, Table 2) (Sack et al., 2011). However, the CARM1–1 complex is distinct for multiple configurations of its ligand and interactions via its 6′-methyleneamine moiety (Figure 4b–d, Figure 4—figure supplement 1). In the CARM1–1 complex, 1 can adopt four alternative configurations (Configuration I in Chains B, D; Configuration II in Chain C; Configuration III and IV in Chain A) accompanied with the structural accommodation of the adjacent residues and water hydrogen bonds (Figure 4b–d, Supplementary file 1-Table B–D). By contrast, only a single configuration of the ligands was observed in SAH- or SNF-bound CARM1 (Figure 4c,d, PDB: 2Y1X, 2Y1W) (Sack et al., 2011).

Detailed structural comparison of CARM1 in complex with SNF, SAH and 1 further revealed that 1 maintains common interactions observed in the CARM1–SNF and CARM1–SAH complexes with several exceptions (Figure 4c,d, Supplementary file 1-Table B–D). Most noticeably, the CARM1–1 complex gains the strong hydrogen bonds via the 6′-methyleneamine moiety of the ligand with (i) the backbone carbonyl of CARM1’s Glu258 (Configuration I, II in Chains B, C, D and Configuration III in Chain A) or (ii) the side chain of Tyr154 (Configuration IV in Chain A), together with several less conserved water hydrogen bonds (Figure 4c,d, Supplementary file 1-Table B–D). By contrast, the 6′-amine of SNF in the CARM1–SNF complex forms weaker hydrogen bonds with Glu258 and may fewer water hydrogen bonds (Figure 4c, Supplementary file 1-Table B, C, PDB: 2Y1W). Comparable interactions are completely absent from the CARM1–SAH complex (Figure 4d, Supplementary file 1-Table B–D, PDB: 2Y1X). The desired hydrogen-bond networks of the 6′-methyleneamine moiety of 1 with CARM1, which are present in the CARM1-1 complex but absent from the CARM1–SNF and CARM1–SAH complexes, can rationalize the significant decrease of IC₅₀ from SNF and SAH to 1.

Another key difference among CARM1–1, CARM1–SNF and CARM1–SAH complexes lies in the region around the carboxylate moiety of these ligands. In Chains A and C of the CARM1–1 complex, the carboxylate moiety of the ligand forms an ionic bond with Arg169 and a hydrogen bond with Gln160 (Figure 4b,c,d, Supplementary file 1-Table B, C). Such interactions are absent from CARM1–SNF and CARM1–SAH complexes (Figure 4d). By contrast, in Chains B and D of the CARM1–1 complex, the same carboxylate moiety forms the ionic bonds with Arg169 and a water hydrogen bond (Figure 4b,c,d, Supplementary file 1-Table B, C). To accommodate the latter conformation, the Gln160 residue flips toward the 3′-ribosyl hydroxyl moiety of 1 to form a new hydrogen bond (Figure 4b,c, Supplementary file 1-Table B, C). Similar interaction patterns can also be found in the CARM1–SNF and CARM1–SAH complexes (Figure 4, Supplementary file 1-Table B–D).

With regards to the rest of the CARM1–ligand interactions, the CARM1 complexes with 1, SAH and SNF are nearly identical except for slightly altered water hydrogen bonds (Figure 4, Supplementary file 1-Table S2–S4). Here, the α-amino moiety of these ligands forms hydrogen bonds with the carbonyl backbone of Gly193, as well as two water hydrogen bonds; their 2′,3′-ribosyl hydroxyl groups form two hydrogen bonds with the side chain of CARM1’s Glu215; adenine’s N1 and N6 form the hydrogen bonds with Asn243 and Glu244/Ser272, respectively; and the adenine ring of these ligands is buried within a hydrophobic pocket. By contrast, there are fewer conserved water hydrogen bonds, such as those involved with the carboxylate and 3′-ribosyl hydroxyl moieties of 1 in Chain A of the CARM1–1 complex (Figure 4, Supplementary file 1-Table C). By contrast, adenine-N7 in the CARM1–SNF and CARM1–SAH complexes forms water hydrogen bonds bridged to Ser272, which are absent from the CARM1–1 complex (Figure 4, Supplementary file 1-Table C, D). Collectively, the general high affinity of 1, SNF and SAH (Figure 4, Supplementary file 1-Table B–D) arises from the combined hydrophilic and hydrophobic interactions of these ligands with CARM1. However, in comparison with SNF and SAH, 1 gains the extra interactions via its 6′-methyleneamine moiety (Figure 4c,d, Supplementary file 1-Table B–D). In addition, 1 adopts the canonical pose with its α-amino carboxylate moiety interacting with Arg168, which is similar to that of SNF and SAH but different from the noncanonical pose of 2a and 5a, upon binding CARM1 (Figure 4d).

Although the in vitro characterization demonstrated the potency and selectivity of 2a and 5a against CARM1, we anticipated their poor membrane permeability as observed for structurally related analogs such as SAH and SNF (Figure 1a) (Boriack-Sjodin et al., 2016; Sack et al., 2011). The lack of membrane penetration is probably due to their primary amine moiety, which has pKa of ~10 and is fully protonated at a physiological pH of 7.4. Given the essential roles of the 9′−amine moiety of 2a and 5a in CARM1 binding (Figure 3e), we envisioned overcoming the membrane permeability issue through a pro-drug strategy by cloaking this amine moiety with a redox-triggered trimethyl-locked quinone butanoate moiety (TML, Figure 5a) (Levine and Raines, 2012). We thus prepared 6a and its control compound 6b by derivatizing 5a and 5b with the TML moiety (Figure 1b, Figure 1—figure supplements 1 and 2). To assess the cellular activity of 6a, we relied on our prior knowledge that CARM1 methylates the Arg1064 of BAF155, a core component of the SWI/SNF chromatin-remodeling complex, and CARM1 knockout abolishes this posttranslational modification in MCF-7 cells (Wang et al., 2014a). Treatment of MCF-7 cells with 10 µM of 6a fully suppressed this methylation mark, whereas treatment with 2a and 5a did not affect this mark (Figure 5b). We thus demonstrated the prodrug-like cellular activity of 6a.

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To further evaluate 6a as a chemical probe against CARM1, we quantified the efficiency by which 6a engages CARM1 in a cellular context and thus suppresses the CARM1-dependent invasion by breast cancer cells. Because of the pro-drug character of 6a and its control compound 6b, we first developed quantitative LC-MS/MS methods to examine their cellular fates for CARM1 engagement (see Materials and methods). Upon treatment of MDA-MB-231 cells with 6a, we observed its time- and dose-dependent intracellular accumulation (Figure 5c, Figure 5—figure supplements 1 and 2). We anticipated the conversion of the pro-drug 6a into 5a, but a striking finding is that 6a can also be readily processed into 2a inside cells (Figure 5c, Figure 5—figure supplements 1 and 2). Remarkably, >100 μM of 2a can be accumulated inside cells for 2 days after 6 hr treatment with a single dose of 5‒10 µM 6a. This observation probably reflects a slow efflux and thus effective intracellular retention of 2a due to its polar α-amino acid zwitterion moiety. Given that cellular CARM1 inhibition is involved with multiple species (2a, 5a and 6a) in competition with SAM, we modeled the ligand occupancy of cellular CARM1 on the basis of their K_d values (K_d,2a=17 nM, K_d,5a=9 nM, K_d,6a=0.28 µM and K_d,SAM≈K_m,SAM=0.25 µM) and MS-quantified intracellular concentrations (Figure 5d, Figure 5—figure supplement 3, Equations 5–7, see Materials and methods). The SAM cofactor, whose intracellular concentration was determined to be 89 ± 16 µM (Figure 5c,d), is expected to occupy >99.5% CARM1 with residual <0.5% as the apo-enzyme under a native setting. With single doses of 6a of 2.5‒10 µM, the combined CARM1 occupancy by 2a, 5a and their pro-drug precursor 6a rapidly reached the plateau of >95% within 6 hr, and was maintained at this level for at least 48 hr (Figure 5e, Figure 5—figure supplements 1 and 2). Notably, treatment with 6a concentrations as low as 0.5 µM is sufficient to reach 60% target engagement within 10 hr and to maintain this occupancy for 48 hr (Figure 5e, Figure 5—figure supplements 1 and 2). The time- and dose-dependent progression of the CARM1 occupancy by these ligands thus provides quantitative guidance upon the treatment of MDA-MB-231 cells with 6a.

Given that 2a is the predominant metabolic product of 6a within cells (Figure 5c,e) and also shows certain affinity to SMYD2 (~10 fold higher IC₅₀ in comparison with CARM1, Figure 1c, Supplementary file 1-Table A), we evaluated SMYD2 engagement of 2a for its potential off-target effect. In a similar manner to that described for the ligand occupancy of cellular CARM1, we modeled the occupancy of cellular SMYD2 by 2a on the basis of K_d,2a=150 nM and K_d,SAM=60 nM for SMYD2 (Figure 5e, Figure 5—figure supplement 4, Materials and methods). Largely because of the high affinity of 2a to SAM and thus a 37-fold larger K_d,2a/K_d,SAM ratio of SMYD2 relative to CARM1 (K_d,2a/K_d,SAM of 2.5 and 0.068 for SMYD2 and CARM1, respectively), the occupancy of SMYD2 by 2a is below 20% (Figure 5e, Figure 5—figure supplement 4) under the efficacy doses of 6a (see cellular data for 6a below). We were thus less concerned about the SMYD2-associated off-target effect under our assay conditions.

The metabolic stability of 6a was also evaluated with a microsomal stability assay (Figure 5c,e, Figure 5—figure supplement 5, see Materials and methods). In the presence of rat liver microsomes, 6a showed decent stability with 24% residual 6a after one-hour incubation. Here, the conversion of 6a into 5a accounted for 40% of the microsome-processed 6a; no production of 2a was detected. Such observation suggests that NQO1, the putative enzyme candidate to reduce the TML moiety in 6a or 6b, is present in microsomes as well as in tumor cells (Dias et al., 2018; Huang et al., 2016). By contrast, peptidase enzymes that are expected to process 5a into 2a are absent from microsomes but rich in tumor cells.

We then conducted a cellular thermal shift assay (CETSA), in which ligand binding is expected to increase CARM1’s thermal stability in a cellular context (Jafari et al., 2014). Our data showed that the treatment of MDA-MB-231 cells with 6a but with not the control compound 6b increased cellular T_m and thus the thermal stability of CARM1 by 4.3 ± 0.6°C (Figure 5f). The distinct effect of 6a in contrast to 6b on the cellular T_m of CARM1 aligns well with the 4.1‒6.2°C difference in the in vitro T_m of CARM1 upon binding 2a and 5a versus SAM (Figure 2e). Here, 6b can penetrate cell membranes and be processed into 5b and 2b in a similar manner as 6a (Figure 5—figure supplement 6). These observations thus present the cellular evidence to show that CARM1 engages 2a and 5a.

To further characterize 6a as a CARM1 chemical probe, we examined the Arg1064 methylation of BAF155 and the Arg455/Arg460 methylation of PABP1, two well-characterized cellular methylation marks of CARM1, upon treating MDA-MB-231 cells with 6a (Lee and Bedford, 2002; Wang et al., 2014a). These methylation marks can be fully suppressed by 6a in a dose-dependent manner (Figure 6a). The resultant EC₅₀ values of 0.45‒0.75 µM (Figure 6b) are well correlated with the modeled 60% cellular occupancy of CARM1 upon treatment with 0.5 µM 6a for 48 hr (Figure 5e). By contrast, the treatment of the negative control compound 6b showed no effect on these methylation marks (Figure 6a). We therefore demonstrated the robust use of 6a (SKI-73) as a CARM1 chemical probe and of 6b (SKI-73N) as its control compound.

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After demonstrating the utility of SKI-73 (6a) as a chemical probe for CARM1, we examined whether chemical inhibition of CARM1 can recapitulate biological outcomes that are associated with CARM1 knockout (CARM1-KO) (Wang et al., 2014a) . Our prior work showed that CARM1’s methyltransferase activity is required for invasion of MDA-MB-231 cells (Wang et al., 2014a). We thus conducted a matrigel invasion assay with MDA-MB-231 cells in the presence of 6a. Relative to the control treatment with DMSO, treatment with SKI-73 (6a) but not its negative control compound SKI-73N (6b) suppressed the invasion of MDA-MB-231 cells (EC₅₀ = 1.3 µM) (Figure 6c,d). The treatment with ≥10 µM 6a produced the maximal 80% suppression of the invasion by MDA-MB-231 relative to the DMSO control, which is comparable with the phenotype of CARM1-KO (Figure 6e). Critically, no further inhibition by 6a on the invasiveness was observed upon 6a treatment (in comparison with the treatment with DMSO or 6b treatment) of MDA-MB-231 CARM1-KO cells (Figure 6e). Notably, treatment with 6a and 6b under the current condition has no apparent impact on the proliferation of parental or CARM1-KO MDA-MB-231 cells (Figure 6—figure supplement 1), consistent with the intact proliferation upon treatment with other CARM1 chemical probes (Drew et al., 2017; Greenblatt et al., 2018; Nakayama et al., 2018). These results suggest that SKI-73 (6a) and CARM1 knockout perturb the common, proliferation-independent biological process and then suppresses 80% of the invasiveness of MDA-MB-231 cells. We thus characterized SKI-73 (6a) as a chemical probe that can be used to interrogate the CARM1-dependent invasion of breast cancer cells.

Because of the advancement of scRNA-seq technology, stunning subpopulation heterogeneity has been uncovered even for well-defined cellular types (Tanay and Regev, 2017). In the context of tumor metastasis, including its initial invasion step, epigenetic plasticity is required to allow a small subset of tumor cells to adapt distinct transcriptional cues for neo-properties (Chatterjee et al., 2018; Flavahan et al., 2017; Wu et al., 2019). To explore the feasibility of dissecting the CARM1-dependent, invasion-prone subset of MDA-MB-231 breast cancer cells, we formulated a cell-cycle-aware algorithm of scRNA-seq analysis and dissected those subpopulations that were sensitive to CARM1 perturbation (Figure 7a, see Materials and methods). Here we conducted 10 × Genomics droplet-based scRNA-seq of 3232, 3583 and 4099 individual cells (a total of 10,914 cells) exposed to 48 hr treatment with SKI-73 (6a), SKI-73N (6b) and DMSO, respectively. Guided by Silhouette analysis, cell-cycle-associated transcripts were identified as dominant signatures of subpopulations (Figure 7—figure supplements 1–18). These signatures naturally exist for proliferative cells and are not expected to be specific for the invasive phenotype. To dissect the subpopulation-associated transcriptomic signatures of invasive cells, we included one additional layer for hierarchical clustering by first classifying the individual cells into G₀/G₁, S, and G₂/M stages (6885, 1520 and 2509 cells, respectively) (Figure 7—figure supplement 6, Supplementary file 1-Table E), and then conducted the unsupervised clustering within each cell-cycle-aware subset (Figure 7b, Figure 7—figure supplements 19–30, Supplementary file 1-Table E). To resolve the subpopulations without redundant clustering, we developed an entropy analysis method and relied on the Fisher Exact test (see Materials and methods). The optimal scores of the combined methods were implemented to determine the numbers of cluster for each subset (Figure 7b, Figure 7—figure supplements 20, 24 and 28) (Butler et al., 2018). The cell-cycle-aware algorithm allowed the clustering of these cells according to the three cell cycle stages under the three treatment conditions and resulted in 21, 7 and 6 subpopulations in G₀/G₁, S, and G₂/M phases, respectively (Figure 7b, Figure 7—figure supplements 21, 25 and 29, Supplementary file 1-Tables F–H). Notably, the 48 hr treatments with SKI-73 (6a) or SKI-73N (6b) had no effect on the cell cycle, as indicated by their comparable cell-cycle distribution patterns (Figure 7—figure supplement 6; Supplementary file 1-Table E), a finding that is consistent with intact proliferation after all three treatments (Figure 6—figure supplement 1).

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With the 21, 7 and 6 subpopulations clustered into the G₀/G₁, S, and G₂/M stages, respectively, we then conducted population analysis, comparing SKI-73 (6a) and SKI-73N (6b) against DMSO (Figure 7c, Figure 7—figure supplements 31 and 32, Supplementary file 1-Table F–H). These subpopulations can be readily classified into five distinct categories according to their cell-cycle-aware responses to SKI-73 (6a) and SKI-73N (6b) treatment: commonly resistant/emerging/depleted versus differentially depleted/emerging (SKI-73/SKI-73N- or 6a/6b-specific) (Figure 7c, Figure 7—figure supplements 31 and 32, Supplementary file 1-Table F–H). Here, we are particularly interested in the SKI-73(6a)-specific depleted subpopulations (Subpopulation 0/2/8/11/13/14/17/19 of G₀/G₁-phase cells and 3 of S-phase cells) as the potential invasion-associated subpopulations, given their sensitivity to SKI-73 (6a) but not its control compound SKI-73N (6b). The subpopulations that remain unchanged after the treatment with SKI-73 (6a) or SKI-73N (6b) (Subpopulation 1/7/12/15 of G₀/G₁-phase cells; 2/4/5 of S-phase cells; 1 of G₂/M-phase cells) were defined as the common resistant subset. SKI-73(6a)-specific emerging subpopulations (Subpopulation 3/4/5/6/16 of G₀/G₁-phase cells; 6 of S-phase cells; 4 of G₂/M-phase cells) are expected to be suppressed by CARM1 but emerge upon its inhibition. The remaining subpopulations are either associated with the effects of the small-molecule scaffold of SKI-73 (6a)/SKI-73N (6b) (commonly emerging Subpopulation 9 of G₀/G₁-phase cells, 0/5 of G₂/M-phase cells; commonly depleted Subpopulation 2/3 of G₂/M-phase cells) or with SKI-73N (6b)-specific effects (differentially depleted Subpopulation 10/18 of G₀/G₁-phase cells, 0 of S-phase cells; differentially emerging Subpopulation 20 of G₀/G₁-phase cells). Interestingly, scRNA-seq analysis of CARM1-KO cells (in comparison with SKI-73 (6a)-treated cells)suggests that CARM1 knockout has more profound effects on the overall landscape of epigenetic plasticity (Figure 7d, Figure 7—figure supplement 33). Collectively, the chemical probe SKI-73 (6a) alters the epigenetic plasticity of MDA-MB-231 breast cancer cells via the combined effects of SKI-73(6a)’s molecular scaffold and specific inhibition of CARM1’s methyltransferase activity.

Given that SKI-73 (6a) has no effect on the cell cycle and proliferation of MDA-MB-231 cells under the current treatment dose and duration, we envision that the invasion capability of MDA-MB-231 cells mainly arises from an invasion-prone subset, 80% of which is depleted by SKI-73 (6a) treatment (Figure 6c–e). We thus focused on Subpopulations 0/2/8/11/13/14/17/19 of G₀/G₁-phase cells and Subpopulation 3 of S-phase cells: in total nine depleted subpopulations specific for SKI-73 (6a) (Figure 7c, Figure 7—figure supplements 31 and 32, Supplementary file 1-Table F–H). To identify invasion-prone subpopulation(s) among these candidates, we compared the transcriptional signature(s) of these subpopulations with those of cells that freshly invaded through Matrigel within 16 hr. Strikingly, in comparison with the highly heterogenous scRNA-seq signature of the parental MDA-MB-231 cells, the freshly harvested invasive cells (3793 cells for scRNA-seq) are relatively homogeneous, with their subpopulations mainly determined by the cell-cycle-related transcriptomic signatures (Figure 7d, Figure 7—figure supplements 33–37). We then classified the freshly harvested invasive cells into G₀/G₁, S and G₂/M stages (Figure 7—figure supplements 38–40, Supplementary file 1-Table E). Through correlation analysis comparing the invasive cells and the subpopulations within each cell-cycle stage (Figure 7d, Figure 7—figure supplements 39–42), we revealed the subsets whose transcriptional signatures closely relate to those of the invasive cells, including Subpopulations 6/7/8/9/14 in G₀/G₁-phase cells, 0/3 in S-phase cells and 1/2 of G₂/M-phase cells (Supplementary file 1-Table F–K). In the context of population analysis for the nine SKI-73 (6a)-specific depleted subpopulations, Subpopulations 8/14 of G₀/G₁-phase cells and Subpopulation 3 in S-phase are putative invasion-prone candidates. Subpopulation 8 of G₀/G₁-phase cells is the most sensitive and the only subpopulation that can be depleted by around 80% with SKI-73 (6a) treatment (Figure 7c). Given the ~80% suppression and ~20% residual invasion capability upon SKI-73 (6a) treatment, we argue that the invasive phenotype of MDA-MB-231 cells predominantly arises from Subpopulation 8 G₀/G₁-phase cells, which only accounts for ~8% of the parental cells in G₀/G₁ phase (~5% without cell-cycle awareness). Differential expression analysis further revealed the single-cell transcriptional signatures of metastasis-implicated genes (e.g. MORC4, S100A2, RPL39, IFI27, ARF6, CHD11, SDPR and KRT18) that are specific for the G₀/G₁-phase Subpopulation 8 and invasive cells but not for other G₀/G₁-phase invasion-prone candidates such as Subpopulation 6/7/9/14 (Figure 7e, Figure 7—figure supplement 43, Supplementary file 1-Table L). The remaining cells of G₀/G₁-phase Subpopulation 8 after SKI-73 (6a) treatment (Figure 7c,d) together with others (subpopulation-6/7/9/14 in G₀/G₁-phase cells, 0/3 in S-phase cells and 1/2 of G₂/M-phase cells, Figure 7—figure supplements 31, 32, 41, 42) may account for the 20% residual invasion capacity.

In the context of SKI-73 (6a)-specific depletion of G₀/G₁-phase subpopulations, there are SKI-73 (6a)-specific emerging G₀/G₁-phase subpopulations: Subpopulation 3/4/5/6/16 (Figure 7c). Population analysis of G₀/G₁-phase cells further revealed that Subpopulations 4 and 16 account for 90% of the emerging subset upon SKI-73 (6a) treatment (Supplementary file 1-Table F). The transcriptional signatures and probably the associated invasion capability of Subpopulations 4 and 16 are dramatically different from those of the freshly harvested invasive cells and the bulk population of the parental cells, including the invasion-prone Subpopulation 8 (Figure 7b,d). Collectively, either CARM1 knockout or CARM1 inhibition with SKI-73 (6a) alters the epigenetic plasticity in a proliferation-independent manner by replacing the most invasion-prone subpopulation with the non-invasive subpopulation(s) to suppress the invasive phenotype (Figure 7f).

On the basis of a novel small-molecule scaffold, 6′-homosinefungin (HSF), SKI-73 (6a) was developed as a pro-drug-like chemical probe for CARM1 by cloaking the 9′-amine moiety of 5a with the TML moiety. SKI-73N (6b) was developed as a control compound for SKI-73 (6a). The inhibitory activity of SKI-73 (6a) against CARM1 was demonstrated by the ability of SKI-73 (6a) but not SKI-73N (6b) to abolish the cellular methylation marks of CARM1: the Arg1064 methylation of BAF155 and the Arg455/Arg460 methylation of PABP1 (Lee and Bedford, 2002; Wang et al., 2014a). The ready intracellular cleavage of TML is expected for the conversion of SKI-73 and SKI-73N (6a and 6b) into 5a and 5b, respectively, but it is remarkable that SKI-73 and SKI-73N (6a and 6b) can also be efficiently processed into 2a and 2b inside cells. In comparison, 6a showed decent metabolic stability with no production of 2a in the presence of microsomes. Here, 2a and 5a are presented as potent and selective CARM1 inhibitors, whereas their control compounds 2b and 5b interact poorly with CARM1.

Competitive assays with the SAM cofactor and the peptide substrate showed that 2a and 5a act on CARM1 in a SAM-competitive and substrate-noncompetitive manner. The SAM-competitive mode is consistent with the ligand–complex structures of CARM1, in which the SAM binding site is occupied by 2a and 5a. Strikingly, as revealed by their ligand–CARM1 complex structures, 2a and 5a engage CARM1 through noncanonical modes, with their 6′-N-benzyl moieties in the binding pocket that is otherwise occupied by the α-amino carboxylate moiety of conventional SAM analogs such as SAH, SNF and 1. This observation is consistent with the 4.1‒6.5 °C increase in the in vitro and cellular T_m of CARM1 upon binding 2a and 5a, which contrasts with the smaller T_m changes with SAM as a ligand. The distinct modes of interaction of CARM1 with 2a and 5a (Figure 3c,g) also rationalize the CARM1 selectivity of the two SAM analogs over other methyltransferases, including closely related PRMT homologs. Through mathematic modeling using the inputs of the LC-MS/MS-quantified intracellular concentrations and CARM1-binding constants of relevant HSF derivatives and the SAM cofactor, we concluded that high intracellular concentrations of 5a and 2a, and thus efficient CARM1 occupancy, can be achieved rapidly and maintained for several days with a single low dose of SKI-73 (6a). By contrast, the occupancy by 5a and 2a of SMYD2, the next likely engaged target, is below 20% with the efficacious doses of 6a that affect cell invasion. The polar α-amino acid zwitterion moiety of 2a and the polar α-amino moiety of 5a probably account for their accumulation and retention inside cells.

To the best of our knowledge, EZM2302, TP-064, and SKI-73 (also 6a in this work, www.thesgc.org/chemical-probes/SKI-73) and their derivatives are the only selective and cell-active CARM1 inhibitors (Drew et al., 2017; Nakayama et al., 2018). Although the potency, selectivity, on-target engagement and potential off-target effects associated with these compounds have been examined in vitro and in cellular contexts as chemical probes, EZM2302, TP-064, and SKI-73 (6a) are differentiated by their molecular scaffolds and modes of interaction with CARM1 (www.thesgc.org/chemical-probes/SKI-73) (Drew et al., 2017; Nakayama et al., 2018). SKI-73 (6a) is a cofactor analog inhibitor embedding a N6'-homosinefungin moiety to engage the SAM binding site of CARM1 in a cofactor-competitive, substrate-noncompetitive manner; EZM2302 and TP-064 occupy the substrate-binding pocket of CARM1 in a SAH-uncompetitive or SAM-noncompetitive manner (Drew et al., 2017; Nakayama et al., 2018). In particular, the prodrug property of SKI-73 (6a) allows its ready cellular uptake, followed by rapid conversion into its active forms inside cells. The prolonged intracellular CARM1 inhibition further distinguishes SKI-73 (6a) from EZM2302 and TP-064.

With SKI-73 (6a) as a CARM1 chemical probe and SKI-73N (6b) as a control compound, we showed that pharmacological inhibition of CARM1 with SKI-73 (6a), but not SKI-73N (6b), suppressed 80% of the invasion capability of MDA-MB-231 cells. By contrast, the pharmacological inhibition of CARM1 with SKI-73 (6a) had no effect on the proliferation of MDA-MB-231 cells. This result is consistent with the lack of anti-proliferation activities of the other two CARM1 chemical probes, EZM2302 and TP-064, against breast cancer cell lines (Drew et al., 2017; Nakayama et al., 2018). The anti-invasion efficiency of SKI-73 (6a) is in good agreement with the intracellular occupancy and the resulting abolition of several methylation marks of CARM1 upon treatment with SKI-73 (6a). Our prior work showed that the methyltransferase activity of CARM1 is required for breast cancer metastasis (Wang et al., 2014a). Among the diverse cellular substrates of CARM1 (Blanc and Richard, 2017), BAF155—a key component of the SWI/SNF chromatin-remodeling complex–is essential for the invasion of MDA-MB-231 cells (Wang et al., 2014a). Mechanistically, the CARM1-mediated Arg1064 methylation of BAF155 facilitates the recruitment of the SWI/SNF chromatin-remodeling complex to a specific subset of gene loci (Wang et al., 2014a). Replacement of the native CARM1 with its catalytically dead mutant or with an Arg-to-Lys point mutation at the Arg1064 methylation site of BAF155 is sufficient to abolish the invasive capability of breast cancer cells (Wang et al., 2014a). CARM1 inhibition with SKI-73 (6a), but not with its control compound SKI-73N (6b), recapitulates the anti-invasion phenotype associated with the genetic perturbation of CARM1. More importantly, there is no additive effect upon combining CARM1-KO with SKI-73 (6a) treatment, underlying the fact that the two orthogonal approaches target the commonly shared pathway(s) that are essential for the invasion of breast cancer cells. In comparison to SKI-73 (6a), the CARM1 inhibitors EZM2302 and TP-064 demonstrated anti-proliferation effects on hematopoietic cancer cells, in particular multiple myeloma (Drew et al., 2017; Greenblatt et al., 2018; Nakayama et al., 2018). Mechanistically, genetic perturbation of CARM1 in the context of leukemia impairs cell-cycle progression, promotes myeloid differentiation, and ultimately induces apoptosis, probably by targeting pathways of proliferation and cell-cycle progression, that is, E2F-, MYC-, and mTOR-regulated processes (Greenblatt et al., 2018). In comparison, CARM1 inhibition with EZM2302 led to a slightly different phenotype, which includes reduction of RNA stability, E2F target downregulation, and induction of a p53 response signature for senescence. (Greenblatt et al., 2018). Collectively, the effects of CARM1 chemical probes are highly context-dependent, with SKI-73 (6a) having different uses in impairing the invasiveness of breast cancer cells, while TP-064 and EZM2302 have uses in preventing the proliferation of hematopoietic cancer cells.

Given the increased awareness of epigenetic plasticity (Flavahan et al., 2017), we employed the scRNA-seq approach to examine MDA-MB-231 cells and their responses to chemical and genetic perturbation with CARM1. Because of the lack of a prior reference to define subpopulations of MDA-MB-231 cells, we developed a cell-cycle-aware algorithm to cluster the subpopulations with a resolution that was able to dissect subtle changes upon treatment with SKI-73 (6a) versus its control compound SKI-73N (6b) in each cell-cycle stage. Guided by Silhouette analysis, the population entropy analysis and the Fisher Exact test, >10,000 MDA-MB-231 breast cancer cells were classified on the basis of their cell-cycle stages and then clustered into 34 subpopulations. With further annotation of these subpopulations according to their different responses to treatment with SKI-73 (6a) versus SKI-73N (6b), we readily dissected the subpopulations that were altered in a SKI-73(6a)-specific (CARM1-dependent) manner and then identified subsets with transcriptional signatures that are similar to that of the freshly isolated invasive cells. Quantitative analysis of SKI-73 (6a)-depleted subpopulations further revealed the most invasion-prone subpopulation, which accounts for only 5% of the total population but at least 80% of the invasive capability of the parental cells. Collectively, we propose a model in which MDA-MB-231 cells consist of subpopulations, with their epigenetic plasticity (Figure 7f) determined by multiple factors including the CARM1-involved BAF155 methylation (Wang et al., 2014a). SKI-73 (6a) inhibits the methyltransferase activity of CARM1, the Arg1064 methylation of BAF155, and thus the target genes associated with the methylated BAF155. These effects alter the cellular epigenetic landscape by affecting certain subpopulations of MDA-MB-231 cells without any apparent effect on cell cycle and proliferation. In the context of the invasion phenotype of MDA-MB-231 cells, the subset of invasion-prone cells is significantly suppressed upon the treatment with SKI-73 (6a). Essential components that are used to dissect the invasion-prone population in this CARM1-dependent epigenetic plasticity model are the scRNA-seq analysis of sufficient MDA-MB-231 cells (>10,000 cells here), the utility of the freshly isolated invasive cells as the reference, the timing and duration of treatment, and the use of SKI-73N (6b) and DMSO as controls. Interestingly, although the invasion-prone subpopulation is also abolished in the CARM1-KO strain, CARM1-KO reshapes the epigenetic plasticity in a much more profound manner, significantly reducing the subpopulation heterogeneity of MDA-MB-231 cells. The distinct outcomes for the pharmacological and genetic perturbation could be due to their different modes of action: short-term treatment with SKI-73 (6a) versus long-term clonal expansion of CARM1-KO cells. The pharmacological inhibition captures the immediate response, whereas the genetic perturbation reports long-term and potential resistant outcomes. This work thus presents a new paradigm to understand cancer metastasis in the context of epigenetic plasticity and provides guidance for similar analyses in broader contexts: other cell lines, patient-derived xenograft samples, and in vivo mouse models of breast cancer.

SAM- and substrate-dependent IC₅₀ values were determined with the radiometric filter paper assay as described above except in the presence of the varied concentrations of the SAM cofactor and the peptide substrate. The IC₅₀ values of 2a and 5a were obtained in the presence of 0.09, 0.18, 0.37, 0.75, 1.50, 2.25, 3.00, 5.62, and 7.50 µM [³H-Me]-SAM or 0.3, 1.5, 7.5, 15, 30, and 50 µM H3 peptide (aa 1–40). The resultant IC₅₀ values were plotted as a function of the concentrations of SAM and the peptide substrate using GraphPad Prism Software. Given the SAM-competitive character of 2a and 5a, their SAM-dependent IC₅₀ values were then fitted according to Equation 1. Here [SAM] is the concentration of SAM, K_m,SAM is the Michaelis-Menten constant, and K_d is the dissociation constant of the CARM1 inhibitor 2a or 5a. K_d, K_d/K_m,SAM and K_m,SAM can therefore be obtained through the intercept of the y-axis, the slope, and their ratio, respectively, upon fitting Equation 1. Given that 6a showed a much higher IC₅₀ (1.1 ± 0.1 µM, Figure 5—figure supplement 3), the K_d value of 6a (K_d,6a = 0.32 µM) was directly obtained from the IC₅₀ value, the K_m,SAM derived above, and the assayed SAM concentration according to Equation 1.

Full-length CARM1 was used for SPR assay. DNA fragment encoding the full-length CARM1 was cloned into pFB-N-flag-LIC donor plasmid. The resulting plasmid was transformed into DH10Bac-competent E. coli cells (Invitrogen) and a recombinant Bacmid DNA was purified, followed by a recombinant baculovirus generation in Sf9 insect cells. Sf9 cells grown in HyQ SFX insect serum-free medium (ThermoScientific) were infected with 10 mL of P3 viral stocks per 1 L of suspension cell culture and incubated at 27°C using a platform shaker set at 150 revolutions per minute. The cells were collected when viability dropped to 70–80% (~72 hr after infection). Harvested cells were re-suspended in PBS, 1X protease inhibitor cocktail (100X protease inhibitor stock in 70% ethanol containing 0.25 mg/mL aprotinin, 0.25 mg/ml leupeptin, 0.25 mg/mL pepstatin A and 0.25 mg/mL E-64) and 2X Roche complete EDTA-free protease inhibitor cocktail tablet. The cells were lysed chemically by rotating 30 min with NP40 (final concentration of 0.6%) and 50 U/mL benzonase nuclease (Sigma), 2 mM 2-mercaptoethanol and 10% glycerol followed by sonication at frequency of 7 (10′‘on/10′‘off) for 2 min (Sonicator 3000, Misoni). The crude extract was clarified by high-speed centrifugation (60 min at 36,000 × g at 4°C) by Beckman Coulter centrifuge. The recombinant protein was purified by incubating the cleared lysate with anti-FLAG M2 affinity agarose gel (Sigma, Cat # A2220) and then rotating for 3 hr, followed by washing with 10 CV TBS (50 mM Tris-HCl, 150 mM NaCl, pH 7.4) containing 2 mM 2-mercaptoethanol, 1X protease inhibitor cocktail (100X protease inhibitor stock in 70% ethanol containing 0.25 mg/mL aprotinin, 0.25 mg/mL leupeptin, 0.25 mg/mL pepstatin A and 0.25 mg/mL E-64) and 1X Roche complete EDTA-free protease inhibitor cocktail tablet. The recombinant protein was eluted by competitive elution with a solution containing 100 µg/mL FLAG peptide (Sigma, Catalog # F4799) in 20 mM Tris pH:7.4, 150 mM NaCl, 5% glycerol, 3 mM 2-mercaptoethanol. Quality of CARM1 (>95%) was determined by SDS–PAGE. The protein was then concentrated, flash frozen with liquid nitrogen, and stored at −80°C for future use.

SPR analysis was performed using a Biacore T200 (GE Health Sciences Inc) at 25°C. Approximately 5500 response units of CARM1 (amino acids 1–608) were amino-coupled onto a CM5 chip in one flow cell according to the protocol of the manufacturer. Another flow cell was left empty for reference subtraction. SPR analysis was conducted in the HBS-EP buffer (20 mM HEPES pH 7.4, 150 mM NaCl, 3 mM EDTA, 0.05% Tween-20) containing 2% (v/v) DMSO. The stock solutions of five concentrations of compound 2a (24.7, 74.1, 222, 667 and 2000 nM) and four concentrations of 5a (6.2, 18.5, 55.6 and 167 nM) were prepared by serial dilution. Binding kinetic experiments were performed with single cycle kinetics with the contact time of 60 s and off time of 300 s in a flow rate of 30 µL/min. To facilitate complete dissociation of compound for the next cycle, a regeneration step (300 s, 40 µL/min of buffer), a period of stabilization (120 s) and two blank cycles were included between each cycle. Kinetic curve fittings were carried out with a 1:1 binding model or a heterogeneous ligand model using Biacore T200 Evaluation software (GE Health Sciences Inc).

TSA was performed as described previously (Blum et al., 2014; Niesen et al., 2007) to examine the melting temperature (T_m) of CARM1 in the presence or absence of ligands. For each measurement (triplicate of each data point), the assay solution containing 50 mM HEPES-HCl (pH = 8.0), Tween-20 0.005% (v/v), 1 mM TCEP, 0.5 μM CARM1, and 5 μM ligand (SAM, 1, 2a or 5a) was mixed with 5 × SYPRO Orange Protein Gel Stain stock (Sigma Aldrich) in a 96-well PCR plate. The mixture was equilibrated at 25°C in dark for 5 min and then loaded onto Bio-Rad CFX96 Real-Time PCR Detection System. The fluorescence readouts were recorded upon increasing the heating temperature from 25°C to 100°C at a rate of 0.2 °C/s. The raw data of the fluorescence readouts versus the temperatures were exported with CFX software and processed as the percentage of the fluorescent signal normalized between the lowest readout of 0% and the highest readout of 100% within the 25‒100°C region. The melting curves were plotted as the normalized fluorescence (%) versus the heating temperature and fit with a sigmoid curve with GraphPad Prism. The T_m corresponds to the temperature with the 50% relative fluorescent signal in the sigmoidal curve.

A DNA fragment encoding the methyltransferase domain of human CARM1 (residues 140–480) was cloned into a baculovirus expression vector pFBOH-MHL (http://www.thesgc.org/sites/default/files/toronto_vectors/pFBOH-MHL.pdf). The protein was expressed in Sf9 cells as an N-terminal 6 × His tag fusion protein and purified by metal chelating affinity chromatography (TALON resin, Clontech, Mountain View, CA, USA) followed by size-exclusion chromatography (Superdex 200, GE Healthcare). Pooled fractions containing CARM1 were subjected to the treatment of tobacco etch virus to remove the 6 × His tag. The protein was purified to homogeneity by ion-exchange chromatography. Purified CARM1 (6.5 mg/mL) was crystallized with the sitting drop vapor diffusion method at 20°C.

For the CARM1–1 complex, CARM1 was mixed with 1 at a 1:5 molar ratio (protein:ligand) and crystallized with the sitting drop vapor diffusion method at 20°C by mixing 1 µL of the protein solution with 1 µL of the reservoir solution containing 20% PEG3350 and 0.2 M diammonium tartrate. X-ray diffraction data for the CARM1–1 complex were collected at 100 K at beam line 23ID-B of Advanced Photon Source (APS), Argonne National Laboratory. Data sets were processed using the HKL-2000 suite (Otwinowski and Minor, 1997). The structure of the CARM1–1 complex was solved by molecular replacement using MOLREP (Otwinowski and Minor, 1997) with the PDB entry 2V74 as the search template. REFMAC (Emsley and Cowtan, 2004; Murshudov et al., 1997) was used for the structure refinement. Graphics program COOTS4 was used for model building and visualization. Crystal diffraction data and refinement statistics for the structure are displayed in Table 2. To further confirm the electronic densities of the ligand, the total omission electron density map was calculated using SFCHECK from CCP4suite and contoured at 1.0 s (Figure 4—figure supplement 1) (Emsley and Cowtan, 2004; Murshudov et al., 1997).

For the CARM1-5a complex, CARM1 was crystallized with the sitting drop vapor diffusion method at 20°C by mixing 1 µL of protein solution with 1 µL of the reservoir solution containing 25% PEGG3350, 0.1M ammonium sulfate and 0.1 M Hepes (pH = 7.5). The compound 5a (0.2 μL of 10 μM in DMSO) was added to the drops with apo crystals and incubated overnight. X-ray diffraction data for the CARM1-5a complex were collected at 100 K on a Rigaku FR-E superbright X-ray generator. Data were processed using the HKL-3000 suite (Minor et al., 2006). The structure was isomorphous to PDB entry 4IKP, which was used as a starting model. REFMAC (Murshudov et al., 2011) was used for structure refinement. Geometric restraints for compound refinement were prepared with GRADE v.1.102 developed at Global Phasing Ltd. (Cambridge, UK). The COOT graphics program (Emsley et al., 2010) was used for model building and visualization, and MOLPROBITY (Williams et al., 2018) was used for structure validation. To further confirm the electronic densities of the ligand, the total omission electron density map was calculated using SFCHECK from the CCP4suite and contoured at 1.0 s (Figure 3b) (Emsley and Cowtan, 2004; Murshudov et al., 1997).

The ligands were docked into the binding site of CARM1 using the induced-fit docking (IFD) protocol (Sherman et al., 2006) implemented in the Schrodinger suite (release 2016–4). The poses for SNF and 2a were selected according to the IFD scores. Specifically, the results identified two distinct poses for 2a with similar scores but only one pose for SNF. The poses were then further relaxed by all-atom, explicit solvent molecular dynamics (MD) simulations. Herein, CARM1 models in complex with the two ligands were placed into explicit water boxes. A simple point charge (SPC) water model (Berendsen et al., 1981) was used to solvate the system, charges were neutralized, and 0.15 M NaCl was added. The total system size was ∼50,000 atoms. Desmond MD systems (D. E. Shaw Research, New York, NY) with OPLS3 force field (Harder et al., 2016) were used. The system was initially minimized and equilibrated with restraints on the ligand heavy atoms and protein backbone atoms, followed by production runs with all atoms unrestrained. The isothermal-isobaric ensemble was used with constant temperature (310 K) maintained with Langevin dynamics and 1 atm constant pressure achieved using the hybrid Nose-Hoover Langevin piston method (Feller et al., 1995) on a flexible periodic cell. For each CARM1–ligand complex, a 600 ns trajectory was collected.

MCF-7 and MDA-MB-231 (parental and CARM1-KO) cell lines (Wang et al., 2014a) were used after their quality was confirmed with STR profile and standard mycoplasma contamination testing.

Using the standard working curves generated above, the concentration (C_A) of each analyte (6a, 5a, 2a, and SAM) in the MeOH extraction of cell lysates was obtained through the ratio (P_A/P_IS) of the mass peak areas of each analyte (P_A) versus each internal standard (P_IS), and the concentration of the internal standard (C_IS) according to Equation 2. For 6a, 5a, and 2a under each assay condition, three similar C_A values (C_A-6b, C_A-5b, and C_A-2b) were obtained with 6b, 5b and 2b as the internal standards, respectively. An average concentration of the analyte (${\displaystyle {\overline{C}}_A}$) was obtained on the basis of the three concentrations weighted by the mass peak areas of the three internal standards (P_IS,6b, P_IS,5b and P_IS,2b) according to Equation 3:

On the basis of the ${\displaystyle {\overline{C}}_A}$ values of 6a, 5a, and 2a (${\displaystyle {\overline{C}}_{A,\mathbf{6}\mathbf{a}}}$, ${\displaystyle {\overline{C}}_{A,\mathbf{5}\mathbf{a}}}$ and ${\displaystyle {\overline{C}}_{A,\mathbf{2}\mathbf{a}}}$) in the MeOH extraction of cell lysates, the intracellular concentrations of the analyte 6a, 5a, and 2a (C_intra,6a C_intra,5a and C_intra,2a) were calculated according to Equation 4. Here ${\displaystyle {\overline{C}}_{A,\mathbf{a}\mathbf{n}\mathbf{a}\mathbf{l}\mathbf{y}\mathbf{t}\mathbf{e}}}$ is the weighted average of the three concentrations in the MeOH extraction, N is the cell number, and V is the mean volume of cells (µL). The mean volume of MDA-MB-231 cells is 1.3 × 10⁻⁶ µL/cell as reported previously (Coulter et al., 2012). The cell number (N) was determined with a hemocytometer. The concentration of SAM (C_A,SAM) in the MeOH extraction was obtained according to Equation 2, in which ‘X’ is the ratio (P_A,SAM/P_IS,CD3-SAM) of the mass peak areas of SAM (P_A,SAM) versus the internal standard CD₃-SAM (P_IS,CD3-SAM) and ‘Y’ is the ratio (C_A,SAM/C_IS,CD3-SAM) of the concentrations of SAM versus CD₃-SAM in the MeOH extraction. Given the identical LC-MS properties of SAM and CD₃-SAM, C_A,SAM was obtained solely on the basis of the working curve with CD₃-SAM as the internal standard. The intracellular concentration of SAM (C_intra,SAM) was then calculated using Equation 4, in which N is the cell number and V is the mean volume of MDA-MB-231 cells (1.3 × 10⁻⁶ µL/cell).

Similar experimental procedures were carried out to quantify the intracellular concentrations of 6b, 5b, 2b and SAM except that 6b, 5b, and 2b were the analytes and their structurally related 6a, 5a and 2a were used as the internal standards with their C_IS values of 0.125 µM, 0.125 µM, and 0.0125 µM, respectively. For each analyte (6b, 5b, and 2b), three working curves (Figure 5c,e, Figure 5—figure supplement 2) were generated to cover the concentration range of 3.9 nM‒18.0 µM of the analyte (C_A,6b, C_A,5b and C_A,2b) with 6a, 5a and 2a (C_IS-6a, C_IS-5a, and C_IS-2a) as the LC-MS/MS internal standards, respectively.

In a manner similar to that described above for the ligand occupancy of CARM1, the SMYD2 occupancy by 2a was modeled with K_d,SAM = 60 nM, K_d,2a = 150 nM and Equation 6. Here, the K_d,SAM value was reported previously upon developing the activity assay of SMYD2 (Sweis et al., 2015). The K_d,2a value was obtained according to IC₅₀ = [SAM]×K_d/K_d,SAM+K_d, in which [SAM]=K_d,SAM = 60 nM for the IC₅₀ assay and IC₅₀ = 0.3 µM was obtained (Supplementary file 1-Table A). The terms of SMYD2 occupancy by exogenous ligands were ignored given their low concentrations and low affinity relative to that of 2a (Supplementary file 1-Table A).

Potential in vivo clearance of 6a was evaluated in the presence of liver microsomes as previously reported (Hansen et al., 2012). Briefly, 6a was dissolved into 50 mM potassium phosphate buffer (pH 7.4) to a final concentration of 100 μM. To a 0.5 mL Eppendorf vial containing ice-cold potassium phosphate buffer (pH 7.4), we added 5 μL of the 100 μM stock solution of 6a, 3 μL of a freshly prepared NADPH solution (5 mM, Sigma-Aldrich, N7785), and 1.33 μL of freshly thawed rat liver microsomes (Sigma-Aldrich, M9066) to yield assay samples with a final volume of 50 μL. The resulting mixture was immediately vortexed and incubated in a 37°C shaker. At the time interval of 0, 20, 40, and 60 min in triplicates, respective assay samples were quenched by adding 50 μL of ice-cold methanol, vigorously vortexed, and centrifuged with 5,000 g at 4°C for 20 min. From the methanol-quenched sample, 50 μL of supernatant was collected and mixed with 50 μL of 0.1% (v/v) TFA/MeOH solution containing 0.125 µM 6b, 0.125 µM 5b, and 16 µM 2b as the internal standards. The resulting mixture was transferred into a 96-well plate (Agilent, 5042–1386) and stored at −20°C for LC-MS/MS analysis. The microsomal stability of 6a was evaluated via LC-MS/MS quantification of the residual 6a and of two potential microsome-processed products, 5a and 2a, upon quantification of intracellular concentrations of 6a, 5a and 2a (as described above). The amount of 6a was plotted as the percentage of the residual concentration at each time point against its initial concentration at 0 min with GraphPad Prism Software. Potential production of 5a and 2a from 6a was examined in parallel. Interestingly, despite robust accumulation of 5a, no 2a was identified with the detection threshold of 0.02 µM.

For negative controls, 3 μL of 50 mM potassium phosphate buffer (pH 7.4) replaced the freshly prepared NADPH solution; two assay samples at the time interval of 0 and 60 min were collected. Under the current microsomal condition, the concentration of 6a remained the same (10 ± 0.7 μM) and there was no production of 5a or 2a.

MDA-MB-231 cells and MCF-7 parental and CARM1-KO (Wang et al., 2014a) cells were maintained in DMEM (Gibco, Gaithersburg, MD) medium containing 10% FBS (Gibco). These cells were then treated with compounds or with DMSO for 48 hr. The resultant cells were washed twice in phosphate-buffered saline (PBS) and the samples were sonicated in ice-cold RIPA buffer (Thermo, Waltham, MA). The lysates were centrifuged (15,000 g) at 4°C for 15 min. The supernatants were kept with the total protein amount determined with Bradford protein assay (BioRad, Hercules, CA). After quantification, 50 μg of protein from each sample was loaded onto 6% SDS-PAGE and transferred onto a nitrocellulose membrane (PALL, Port Washington, NY). For the Arg1064 methylation mark of BAF155, the blots were blocked in 5% non-fat milk for 1 hr and incubated with anti-me-BAF155 (Cancer Cell, 2014), anti-BAF155 (1:1000; Santa Cruz Biotechnology, Dallas, TX), anti-CARM1 (1:1000; Genemed Synthesis, San Antonio, TX), and anti-β-actin (1:20000; Sigma-Aldrich, St. Louis, MO) overnight at 4°C. After washing three times in Tris-buffered saline with Tween 20 (TBST), the blots were incubated with HRP-conjugated secondary antibody (1:3000; Jackson ImmunoResearch, West Grove, PA). After washing blots with TBST, the membranes were developed using SuperSignal West Pico ECL solution (Thermo). For the Arg455/Arg460 methylation mark of PABP1, anti-me-PABP1 (1:1000) and anti-PABP1 (1:1000) antibodies (Genemed Synthesis, San Antonio, TX) were used instead. Here the antibodies against CARM1, PABP1, and me-PABP1 were custom generated by Genemed Synthesis (San Antonio, TX) (Zeng et al., 2013). The density of the protein bands was quantified using ImageJ software (NIH, Bethesda, MD). The EC₅₀ values were obtained by fitting the methylation percentage (%) of BAF155 or PABP1 against the concentrations of the inhibitor using a sigmoidal equation with GraphPad Prism Software.

CETSA was performed as described previously (Jafari et al., 2014) to examine the intracellular engagement of 6a or 6b with CARM1. Briefly, 2.0 × 10⁶ MDA-MB-231 cells were incubated with 15 μM 6a or 6b and DMSO for 48 hr. The harvested cells were re-suspended in PBS buffer and divided into eight aliquots (30 µL/aliquot), and then heat-shocked at various temperatures (49.1, 54.6, 57.0, 59.5, 61.8, 63.9, 65.6, and 67.0°C) for 3 min with a Bio-Rad CFX96 Real-Time PCR Detection Instrument (using a temperature gradient of 49‒67°C). The heat-shocked cells were then lysed with the freeze-thaw method with a liquid nitrogen bath followed by a 25°C water bath for five cycles. The cell lysate was centrifuged at 4°C at 18,000 g for 20 min. The resultant supernatant containing the soluble protein fraction was collected and loaded onto an SDS-PAGE gel (20 µL). Western blotting of CARM1 was performed with anti-CARM1 antibody (Cell Signaling Technology, C31G9). For each sample, the band intensity of CARM1 was quantified with ImageJ. The band intensity of CARM1 was normalized to the band intensity at 49.1°C (the lowest heat-shock temperature). Melting curves were obtained by plotting the normalized band intensity against the heat-shock temperatures and fit with a Boltzmann sigmoidal equation in GraphPad Prism. The melting temperatures (T_m) of 6a, 6b, or DMSO were obtained as the heat-shock temperatures that correspond to the 50% normalized band intensity in the fitted sigmoidal curves.

MDA-MB-231 parental and CARM1-KO cells (Wang et al., 2014a) were maintained in DMEM (Gibco, Gaithersburg, MD) medium containing 10% FBS (Gibco). Cell invasion assays were performed using 8.0 µm pore size Transwell inserts (Greiner Bio-One, Kremsmünster, Austria). MDA-MB-231 parental and CARM1-KO (Cancer Cell, 2014) cells were harvested with trypsin/EDTA and washed twice with serum-free DMEM (Gibco). 2 × 10⁵ cells in 0.2 mL serum-free DMEM (Gibco) were seeded onto the upper chamber, which was pre-coated with a thin layer of 40 uL of 2 mg/mL Matrigel (Corning, NY, USA) for 2 hr incubation at 37°C. To the lower chamber, we added 0.6 mL DMEM containing 10% FBS (GIBCO) and compounds or DMSO. After 16 hr in the 37°C incubator, the cells on the inner side of the upper chamber together with the Matrigel layer were removed using cotton tips. The residual invasive cells in the outer side of the upper chamber were fixed in 3.7% formaldehyde (a weight percentage) at an ambient temperature (22°C) for 2 min and 100% methanol for 20 min, and then stained for 15 min with a solution containing 1% crystal violet and 2% ethanol in 100 mM borate buffer (pH 9.0). The number of invasive cells was counted under a microscope by taking five independent fields. Relative cell invasion was determined by the number of the invasive cells normalized to the total number of cells adhering to 0.8 µm transwell filters. The EC₅₀ was obtained with GraphPad Prism Software upon fitting Equation 8, in which ‘%Inhibition’ is the percentage of the inhibition of invasiveness, ‘Maximal Inhibition%’ is the percentage of the maximal inhibition of invasiveness, and [Inhibitor] is the concentration of the inhibitor.

To examine proliferation of MDA-MB-231 cells, 5000 cells of parental and CARM1-KO cells were seeded in a 96-well plate and incubated in 37°C overnight. These cells were treated with various doses (0.0001‒10 μM) of SKI-73 or SKI-73N (6a or 6b) in DMSO and incubated for 72 hr. An MTT assay was then performed to examine viability with DMSO-treated cells as the control. The relative viability of compound-treated cells versus DMSO-treated parent cells were plotted against the concentrations of SKI-73 and SKI-73N (6a and 6b).

Cell preparation for scRNA-seq. 10 × Genomics droplet-based scRNA-seq was implemented to characterize five types of MDA-MB-231 cells: MDA-MB-231 cells treated with DMSO, SKI-73 (6a) and SKI-73N (6b), MDA-MB-231 cells that freshly invaded through Matrigel, and CARM1-KO MDA-MB-231 cells. For the first three samples, MDA-MB-231 cells were treated with DMSO, 10 μM SKI-73 (6a), and 10 μM SKI-73N (6b) for 48 hr. The resulting cells were trypsinized at 37°C for 3 min. The harvested cells were washed twice with 1 × PBS (phosphate-buffered saline) containing 0.04% (volume%) bovine serum albumin (BSA), gently dispersed to dissociate cells, and then filtered through a cell strainer (100 μm Nylon mesh, Fisherbrand) to obtain single-cell suspensions for scRNA-seq. For the CARM1-KO sample, the cells were trypsinized at 37°C for 3 min, washed twice with 1 × PBS containing 0.04% BSA, and filtered through a 100 μm Nylon-mesh cell strainer (Fisherbrand) to obtain single-cell suspensions for scRNA-seq.

To collect the cells that freshly invaded through Matrigel, the conditions described above for cell invasion assays were applied to allow approximately 5% of the 1 × 10⁷ seeded MDA-MB-231 cells to invade through Matrigel. Briefly, ten Transwell inserts with a diameter of 24 mm and a pore size of 8.0 μm were pre-coated with a thin layer of 54 μL of 2 mg/mL Matrigel (Corning). 1 × 10⁶ MDA-MB-231 cells in 1.0 mL serum-free DMEM (Gibco) were seeded into the upper chamber of each Matrigel-coated Transwell insert. 2.0 mL DMEM containing 10% FBS (Gibco) was added into the lower chambers. After 16 hr incubation, the cells on the inner side of the upper chamber together with the Matrigel layer were removed using cotton tips. The cells that freshly invaded–those attached on the outer side of the upper chamber–were subjected to 3 min trypsin digestion at 37°C for detachment. The resulting cells were washed twice with 1 × PBS containing 0.04% BSA, gently dispersed to dissociate cells, and filtered through a 100 μm Nylon-mesh cell strainer (Fisherbrand) to obtain single-cell suspensions for scRNA-seq.

The scRNA-seq libraries were prepared following the user guide manual (CG00052 Rev E) provided by the 10 × Genomics and Chromium Single Cell 3' Reagent Kit (v2). Briefly, samples containing approximately 8700 cells (93–97% viability) were encapsulated in microfluidic droplets at a dilution of 66–70 cells/µL, which resulted in 4369–5457 recovered single-cells per sample with a multiplet rate ~3.9%. The resultant emulsion droplets were then broken and barcoded cDNA was purified with DynaBeads, followed by 12-cycles of PCR-amplification: −98 °C for 180 s, 12×(98°C for 15 s, 67°C for 20 s, 72°C for 60 s), and 72°C for 60 s. The 50 ng of PCR-amplified barcoded-cDNA was fragmented with the reagents provided in the kit and purified by SPRI beads with an averaged fragment size of 600 bp. The DNA library was then ligated to the sequencing adapter followed by indexing PCR: −98 °C for 45 s; 12× (98°C for 20 s, 54°C for 30 s, 72°C for 20 s), and 72°C for 60 s. The resulting DNA library was double-size purified (0.6–0.8×) with SPRI beads and sequenced on Illumina NovaSeq platform (R1 – 26 cycles, i7 – eight cycles, R2 – 96 cycles) resulting in 70–79 million reads per sample with average reads per single-cell being 8075–10,342 and average reads per transcript 1.11–1.15.

The fastq files containing the transcriptome and barcoding metadata were demultiplexed using the SEquence Quality Control (SEQC) pipeline (http:github.com/ambrosejcarr/seqc.git) resulting in around 8000 UMIs per one cell. The table of UMI counts was used as the input and Seurat package v.2.3.4 (Butler et al., 2018) was applied for scRNA-seq analysis. Here, the raw UMI counts were normalized per cell by dividing the total number of UMIs in each individual cell, multiplying by a scale factor of 10,000 and transforming into natural logarithm values. Cells with 1000~5000 genes and <20% mitochondrial RNA transcripts were kept for further analysis. Dimensionality reduction was carried out by selecting a set of highly variable genes on the basis of the average expression and dispersion per gene. The set of genes was used for principle component analysis (PCA). Top principle components were then chosen for cell clustering analysis and t-SNE projection. Regression was performed to remove cell–cell variation in gene expression driven by the UMI number, mitochondrial gene content and ribosomal gene content using ‘ScaleData’ function in Seurat package (Nestorowa et al., 2016). Clusters of cells were identified by clustering algorithm based on a shared nearest neighbor (SNN) modularity optimization that was included in Seurat package v.2.3.4 (Butler et al., 2018).

Fisher’s Exact Test was implemented to evaluate the agreement of the clusters with the three cell origins (DMSO-, SKI-73(6a)- or SKI-73N(6b)-treated cells) using R package ‘fisher.test’: http://mathworld.wolfram.com/FishersExactTest.html (Mehta and Patel, 1983). Because of the significant computation cost of Fisher’s Exact Test, the cell population of each Fisher’s Exact Test was down-sampled to 150 cells and this process was repeated for 100 times to cover a majority of the cell population. The p-value of Fisher’s Exact Test was then computed by Monte Carlo simulation. Means and standard errors of p-values were calculated and reported as the outputs of Fisher’s Exact Test.

Three algorithmic scoring systems were used over a range of the resolution parameter that sets the corresponding ‘granularity’ of clustering, with higher values indicating a greater number of clusters. Here, silhouette analysis was applied to determine the number of clusters in an unsupervised manner, without awareness of the three cell origins (DMSO-, SKI-73(6a)- or SKI-73N(6b)-treated cells). The entropy scoring and Fisher’s Exact Test were implemented to evaluate the biological meaning of the clustering, using the minimal cluster number to resolve the cells between the three treatment conditions maximally. Given the awareness of the three cell origins, the minimal number of clusters with the maximal resolution of cell origin guided by the entropy scoring and Fisher’s Exact Test is expected within the 1~3-fold range of the optimized number of clusters guided by Silhouette analysis. Fisher’s Exact Test was used as the primary scoring method to determine the efficiency of clustering, given its higher resolution.

‘d_j,i’ (‘d_DMSO,i’, ‘d_SKI-73N,i’ and ‘d_SKI-73,i’ in Equation 9 are defined as the fraction of the cells with the ‘j’ origin (j = 1, 2 or three for the treatment with DMSO, SKI-73N/6b and SKI-73/6a, respectively) within the ‘i’ subpopulation (i = 0‒n for the clustered subpopulation). ‘d_i,total’ is defined as the fraction of the cells of the ‘i’ subpopulation within the total cell population in each cell-cycle stage. ‘d_(j,i),total =dj_j,i ×d_i,total’ represents the fraction of the cells with the ‘j’ origin (DMSO, SKI-73/6a, and SKI-73N/6b) and the ‘i’ subpopulation within the total cell population in each cell-cycle stage. For a specific subpopulation ‘i’, there are three ‘d_(j,i),total’ values (d_{(DMSO,i),total}, d_{(SKI-73N,i),total} and d_{(SKI-73,i),total}) for the treatments with DMSO, SKI-73N (6b) and SKI-73 (6a), respectively. The alteration of subpopulations is defined as the ratios of d_{(SKI-73N,i),total}/d_{(DMSO,i),total} or d_{(SKI-73,i),total}/d_{(DMSO,i),total} fall out of the range of 1.0 ± 0.2. Population analysis was conducted by classifying the SKI-73N/SKI-73(6a/6b)-treated subpopulations into the following five categories: commonly resistant (0.8 < ‘d_{(SKI-73N,i),total}/d_{(DMSO,i),total}’ and ‘d_{(SKI-73,i),total}/d_{(DMSO,i),total}’<1.2), commonly emerging (‘d_{(SKI-73N,i),total}/d_{(DMSO,i),total}’ and ‘d_{(SKI-73,i),total}/d_{(DMSO,i),total}’≥1.2), commonly depleted (‘d_{(SKI-73N,i),total}/d_{(DMSO,i),total}’ and ‘d_{(SKI-73,i),total}/d_{(DMSO,i),total}’≤0.8; ∣‘d_{(SKI-73N,i),total}/d_{(DMSO,i),total}’−‘d_{(SKI-73,i),total}/d_{(DMSO,i),total}’∣<0.15), differentially emerging (either ‘d_{(SKI-73N,i),total}/d_{(DMSO,i),total}’ or ‘d_{(SKI-73,i),total}/d_{(DMSO,i),total}’>1.2), and differentially depleted (‘d_{(SKI-73N,i),total}/d_{(DMSO,i),total}’ or ‘d_{(SKI-73,i),total}/d_{(DMSO,i),total}’<0.8; ∣‘d_{(SKI-73N,i),total}/d_{(DMSO,i),total}’−‘d_{(SKI-73,i),total}/d_{(DMSO,i),total}’∣>0.15). Although additional combinations of differentially altered subpopulations could be possible, only those defined above were found under our treatment conditions.

In each cell cycle (G₀/G₁, S and G₂/M) of the cells treated with DMSO, SKI-73 (6a) or SKI-73N (6b) and ‘invasion cells’, correlation analysis of subpopulations was conducted with ‘BuildClusterTree’ function in the Seurat package (https://rdrr.io/cran/Seurat/man/BuildClusterTree.html) (Nestorowa et al., 2016). The phylogenetic trees were constructed by averaging gene expressions across all cells in each subpopulation and then calculating distance on the basis of expressions averaged between different subpopulations.

Differentially expressed genes were identified by comparing two groups of cells using the Wilcox rank sumtest with the ‘FindMarkers’ function in the Seurat package (Nestorowa et al., 2016). In particular, the ‘invasion cells’ and their most correlated clusters (which were revealed in the correlation analysis) were selected as the ‘high’ group; the remaining remotely related clusters were selected as the ‘low’ group. The differential expression analysis was then performed by comparing cells in the ‘high’ group with the cells in the ‘low’ group. For the G₀/G₁-phase cells, the ‘invasion cells’ and Subpopulation 6, 7, 8, 9, 14 were selected as the ‘high’ group; Subpopulation 0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20 were selected as the ‘low’ group. For the G_2/M-phase cells, the ‘invasion cells’ and Subpopulations 1, 2 were selected as the ‘high’ group; and Subpopulations 0, 3, 4, 5 were selected as the ‘low’ group. For the S-phase cells, the ‘invasion cells’ and Subpopulations 0, 3 were selected as the ‘high’ group; and Subpopulations 1, 2, 4, 5, 6 were selected as the ‘low’ group. Differentially expressed genes were ranked according to the average log₂ fold change ‘avg_logFC’ and the adjusted p-values ‘p_val_adj’ with the Seurat package. Top upregulated and downregulated genes were chosen by setting a cutoff on their ‘avg_logFC’ values (>0.25 or <−0.25). Then, curated genes with potential functional relevance to cancer malignancy (30 upregulated and 10 downregulated genes) were selected as representative genes for generating heat map plots using the ‘DoHeatmap’ function in the Seurat package.

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

The authors thank Christina Leslie for suggesting scRNA-seq analysis. Funding has been provided by the US National Institutes of Health (ML: R01GM096056, R01GM120570, R35GM131858), the US National Cancer Institute (ML: 5P30 CA008748; WX: R01CA236356, R01CA213293; LXQ: CA214845, CA008748), the Starr Cancer Consortium (ML), the MSKCC Functional Genomics Initiative (ML), the Sloan Kettering Institute (ML), the Mr. William H Goodwin and Mrs. Alice Goodwin Commonwealth Foundation for Cancer Research, the Experimental Therapeutics Center of Memorial Sloan Kettering Cancer Center (ML), the MSKCC Metastasis and Tumor Ecosystems Center (ML), the Tri-Institutional PhD Program in Chemical Biology (SC), the Susan G Komen Foundation (EJK: PDF17481306), and Special Funding of Beijing Municipal Administration of Hospitals Clinical Medicine Development (YangFan Project) (ZZ: ZYLX201713). The Structural Genomics Consortium is a registered charity (no. 1097737) that receives funds from AbbVie, Bayer Pharma AG, Boehringer Ingelheim, the Canada Foundation for Innovation, the Eshelman Institute for Innovation, Genome Canada, the Innovative Medicines Initiative (EU/EFPIA) (ULTRA-DD grant no. 115766); Janssen, Merck KGaA (Darmstadt, Germany), MSD, Novartis Pharma AG, the Ontario Ministry of Economic Development and Innovation, Pfizer, the São Paulo Research Foundation-FAPESP, Takeda, and the Wellcome Trust. The X-ray structure results for CARM1 are derived from work performed at Argonne National Laboratory, Structural Biology Center (SBC) at the Advanced Photon Source. SBC-CAT is operated by U Chicago Argonne, LLC, for the US Department of Energy, Office of Biological and Environmental Research under contract DE-AC02-06CH11357. These experiments were performed using beamline 08ID-1 at the Canadian Light Source, which is supported by the Canada Foundation for Innovation, Natural Sciences and Engineering Research Council of Canada, the University of Saskatchewan, the Government of Saskatchewan, Western Economic Diversification Canada, the National Research Council Canada, and the Canadian Institutes of Health Research.

Dr. Zhang unfortunately passed away during the revision of this manuscript. 

© 2019, Cai et al.

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