PRMT5 Is a Critical Regulator of Breast Cancer Stem Cell Function via Histone Methylation and FOXP1 Expression

PRMT5, but Not PRMT1, Is Functionally Required for In Vitro BCSC Function in ER⁺ Breast Cancers

PRMT1 and PRMT5 have been increasingly linked to stem cell function in normal and cancer cells (Banasavadi-Siddegowda et al., 2017, Blanc et al., 2017, Jin et al., 2016, Liu et al., 2015, Zhang et al., 2015) and breast cancer pathogenesis (Baldwin et al., 2012, Chen et al., 2017, Goulet et al., 2007, Powers et al., 2011, Yang et al., 2015). Whilst depletion of PRMT5 reduces the proliferation of bulk MCF7 breast cancer cells (Figure S1A; Scoumanne et al., 2009), no study has yet examined whether PRMT1 and PRMT5 also regulate the BCSC population. To address this, we exploited the fact that breast cancer cell lines possess a small population of cells that molecularly and functionally behave as cancer stem cells (Harrison et al., 2010, Ponti et al., 2005). Two approaches were used to isolate this population: flow cytometry gating on ESA⁺CD24^lowCD44⁺ (Figure S1B) and the isolation of viable MCF7 cells after 16 hr suspension culture on poly-HEMA-coated plates to prevent cell attachment (Figure S1C). These anoikis-resistant (AR) cells are significantly enriched in stem cell markers compared with their monolayer counterpart and have tumor-initiating capacities (Harrison et al., 2010). Although PRMT1 levels remained the same, PRMT5 expression was significantly elevated within the AR or BCSC population (Figures 1A and 1B). To investigate the significance of this, we generated two PRMT1 and PRMT5-knockdown MCF7 cell lines each expressing distinct short hairpin RNA (shRNA) sequences (shPRMT1[1] and shPRMT1[2]; shPRMT5[1] and shPRMT5[2]; Figure 1C) and analyzed their ability to form mammospheres, a measure of the number and proliferative potential of tumor-initiating cells in vitro (Ponti et al., 2005). Depletion of either PRMT1 or PRMT5 reduced primary mammosphere formation, indicative of either reduced stem cell/progenitor proliferation or a reduction in the number of tumor-initiating cells, but only depletion of PRMT5 led to a further reduction in secondary mammospheres, suggesting self-renewal defects (Figure 1C). Thus, it appears that although both PRMT1 and PRMT5 are required for BCSC proliferation and production of progenitor cells, only PRMT5 is required for BCSC self-renewal. To validate these findings, we repeated these experiments in a second ER⁺ breast cancer cell line, T47D (Figure 1D), and analyzed stem cell numbers by ALDEFLUOR staining, an alternative marker of BCSCs (Ginestier et al., 2007). As depletion of PRMT5 also reduced the proportion of ALDEFLUOR⁺ T47D cells (Figure 1E), our data strongly imply that PRMT5 is required for maintaining BCSC function in vitro.

Amplification and overexpression of PRMT5 in breast cancer is associated with reduced patient survival rates (Figures S1D and S1E) (Cerami et al., 2012, Gao et al., 2013, Györffy et al., 2010). Since chromatin-modifying enzymes are known to regulate cellular events that can lead to the conversion of non-CSCs toward a CSC-like phenotype and the expansion of the BCSC pool (Chang et al., 2011, Tam and Weinberg, 2013), we next asked whether overexpression of active PRMT5 by co-expressing PRMT5 and its essential cofactor MEP50 was sufficient to promote a BCSC phenotype. As expected, co-expression of PRMT5 requires MEP50 for elevated symmetric dimethylation levels (Figures 1F, S1F, and S1G). Accordingly, overexpression of PRMT5 alone had no significant effect on primary mammosphere numbers, whereas co-expression of PRMT5 and MEP50 significantly increased both primary and secondary mammosphere numbers (Figure 1G). Interestingly, co-overexpression of catalytically inactive PRMT5 (PRMT5-G367A/R368A) (Pal et al., 2004) with MEP50 failed to stimulate BCSC activity (Figures 1F and 1G). These findings therefore imply that PRMT5 drives BCSC proliferation and self-renewal via the methylation of target substrates.

PRMT5 Is Required for In Vivo BCSC Maintenance

The gold-standard in vivo assay to determine tumor-initiating capacity of putative BCSCs is limiting dilution analysis. Here, groups of NSG (NOD/Scid/IL-2Rγnull) mice were subcutaneously injected with five different dilutions (5 × 10⁶ to 5 × 10⁴) of unsorted cells and monitored for tumor growth, the premise being that the more tumor-initiating cells present within the bulk tumor cell population, the fewer cells required to generate a tumor (Figure 2A). After 20 days, control animals from the 5 × 10⁶ cell group reached license limit, and all mice were scored for the presence of tumors >0.1 cm³ as evidence of tumor initiation. Depletion of PRMT5 clearly showed a reduction in the potential to form tumors at all cell numbers injected, becoming more evident with small cell numbers. For example, whereas 4 of 7 mice (57%) injected with 5 × 10⁴ shCTRL cells developed tumors, only 1 of 11 mice (9.1%) injected with the same number of shPRMT5 cells did so. Strikingly, using L-Calc (Stem Cell Technologies) to calculate stem cell frequency, we show that depletion of PRMT5 reduced cancer stem cell numbers from 1:187,878 to 1:1,042,530, a 5.5-fold reduction (Figure 2B). In order to determine the effects of PRMT5 depletion on BCSC and tumor biology, mice in each group were aged and sacrificed when control animals reached license limit. Tumors were excised and analyzed for stem cell function by mammosphere assay. Importantly, the reduction in stem cell frequency was reflected ex vivo, as PRMT5-depleted cells from excised tumors displayed reduced proliferation and self-renewal characteristics (Figure 2C). Consistent with a reduction in stem cells, we observed that PRMT5-depleted tumors were less proliferative, as indicated by differences in final tumor weight, BrdU incorporation, and tumor growth rate (Figures 2D–2F and S2). Conversely, overexpression of active PRMT5 in limiting dilution xenografts increased stem cell numbers by 5.91-fold (Figures 2G, 2H, S3A, and S3B), which was reflected ex vivo by mammosphere assay (Figure 2H). Together, this in vivo analysis clearly shows that elevated levels of active PRMT5 are sufficient for BCSC activity.

Although our limiting dilution analysis demonstrates an important role for PRMT5 in regulating BCSCs, PRMT5 is also known to promote the proliferation of bulk breast cancer cells (Figure S1A; Scoumanne et al., 2009). In line with this, depletion of PRMT5 reduces both the in vitro and in vivo proliferation of isolated BCSCs and the differentiated population (Figures S3C–S3H). Importantly, and in agreement with our limiting dilution analysis using bulk cell population (Figures 2B and 2G), depletion of PRMT5 affected the tumor-initiating capacity of only ESA⁺CD24^lowCD44⁺ BCSCs (Figure S3E), not the differentiated population (Figure S3G). Taken together, these results imply that PRMT5 has multiple roles in breast cancer growth, regulating both tumor-initiating and more differentiated cells, and that drug targeting of PRMT5 could potentially affect the survival of both cell populations.

To investigate the impact of PRMT5 depletion on tumor biology, we performed histological analysis of excised tumors in collaboration with a breast cancer pathologist and scored for pathological features currently used in patient diagnosis. We observed that PRMT5-depleted tumors displayed reduced cellularity, increased fibrosis, and tubule formation, consistent with a less aggressive phenotype (Figures 3A, 3B, and S4A). Control tumors often exhibited high cellularity and large areas of clear cell differentiation (Figure 3E), a phenotype of a particularly aggressive breast cancer subtype. Areas of necrosis, another feature of large, rapidly growing tumors, were also observed in shCTRL tumors (Figures 3C and 3D). These features were rarely exhibited in PRMT5-depleted tumors, correlating with their small size. Interestingly, depletion of PRMT5 in AR or ESA⁺CD24^lowCD44⁺ populations did not alter cell cycle or promote apoptosis (Figures 3F and 3G). Hence, given that PRMT5-depleted tumors appear more differentiated with a less aggressive pathology, our findings are consistent with PRMT5 suppressing differentiation and thus facilitating the maintenance of BCSC identity.

PRMT5 Is Required for BCSC Function in Established Tumors

Recently, PRMT5 has become an attractive therapeutic target for the treatment of leukemia and lymphoma, with pre-clinical PRMT5-specific inhibitors displaying impressive in vivo efficacy in murine models of mantle cell lymphoma and chronic myelogenous leukemia (CML) (Chan-Penebre et al., 2015, Jin et al., 2016). However, these studies did not address the effect of suppressing or inhibiting PRMT5 on tumor growth in an organism that had already presented with disease, a critical question if PRMT5 inhibitors are to be a viable therapeutic option. We therefore engineered MCF7 cells to express a doxycycline (dox)-regulated PRMT5 silencing construct (Tet-ON-shPRMT5) in combination with constitutive expression of the luciferase gene enabling in vivo imaging of tumor growth (Figures 4A and 4B). After subcutaneous injection, tumors were allowed to grow to a palpable size (Figure S4B) and in vivo PRMT5 depletion induced by feeding mice dox-supplemented chow (Figures 4A and 4B). Tumors derived from Luc-Tet-ON-shCTRL cells continued to grow for the duration of the experiment. In contrast, in vivo depletion of PRMT5 substantially slowed tumor growth and in some cases caused regression (Figures 4C and 4D). Accordingly, Luc-Tet-ON-shPRMT5-derived tumors were considerably smaller than control tumors (Figures 4E and 4F).

Although these results suggest that PRMT5 is required to sustain the growth of an established carcinoma, we wanted to determine if this was through the maintenance of the BCSC population. We therefore serially transplanted cells derived from Luc-Tet-ON-shCTRL and shPRMT5 tumors and conducted limiting dilution analysis. Excised tumors were dissociated into single cells, and five groups of NSG mice were subcutaneously injected with 1 × 10⁵ to 1 × 10³ tumor-derived cells (Figure 5A). PRMT5 silencing in the transplanted cells was validated by immunoblotting, and tumors were allowed to develop for 40 days. As expected, mice injected with larger numbers of cells were more likely to develop tumors than those injected with small cell numbers (Figure 5C); however, irrespective of cell number, PRMT5-depleted serially transplanted tumors grew at a much slower rate (Figures 5B and 5D). Furthermore, examination of the 1 × 10³ cell group clearly demonstrated that whereas serially transplanted Luc-Tet-ON-shCTRL-derived tumors steadily outgrew, Luc-Tet-ON-shPRMT5-derived tumors cells failed to generate any growths (Figure S4C). These findings strongly indicate that in vivo depletion of PRMT5 alters the functional capacity of tumor-initiating cells. Indeed, by scoring the number of mice that presented with tumors >0.1 cm³ at time of collection (all mice irrespective of group were collected at the same time), Luc-Tet-ON-shPRMT5-derived, serially transplanted tumors displayed a 12-fold reduction in stem cell frequency, from 1:3,555 to 1:43,135, after in vivo PRMT5 depletion (Figure 5C). Consistent with a reduced tumorigenic capacity, PRMT5-depleted xenografts were of a lower cellularity, displayed frequent tubule formation, and were sometimes highly fibrotic, resulting in a greater proportion of tumors with a lower histological grade (Figures 5E, S4D, and S4E). In support, mammosphere analysis of resected and dissociated tumors demonstrated that PRMT5 depletion reduced mammosphere-forming capacity ex vivo (Figure 5F). Taken together, our data are highly suggestive that depletion of PRMT5 in established carcinomas reduces tumor propagation by restricting the number of BCSCs.

PRMT5 Epigenetically Regulates FOXP1 Expression

Because PRMT5 is an established regulator of gene expression (Migliori et al., 2012, Zhao et al., 2009), we hypothesized that one mechanism by which PRMT5 could be regulating BCSC function was through transcriptional control. To investigate this, we isolated three replicates of the ESA⁺CD24^lowCD44⁺ populations from MCF7-shCTRL and shPRMT5 cells and conducted RNA sequencing (RNA-seq) to identify differences in gene expression. Depletion of PRMT5 resulted in 214 significantly differentially regulated genes, of which 136 were upregulated and 78 downregulated (Figures S5A–S5C). KEGG pathway analysis of enriched genes suppressed by PRMT5 (i.e., those that were upregulated after shRNA depletion) identified cancer pathways and signaling pathways (including cGMP-PGK, PI3K-AKT, ErbB, and FoxO pathways) (Figure S5D), while metabolic genes are predominantly induced by PRMT5 (ALDOC, HK2, TSTA3, and ALDH3A1; Figure S5E). Changes in expression of classic stem cell genes such as OCT4 or NANOG were not detected by RNA-seq. However, closer examination by qPCR analysis of AR cells reconstituted with wild-type PRMT5 did imply that they were PRMT5 regulated (Figure S6A). Interestingly, Wnt/β-catenin genes, reported as PRMT5 targets in leukemic stem cells (Jin et al., 2016, Tee et al., 2010), could not be validated by qPCR (Wnt5A, PRICKLE2), implying that the mechanisms by which PRMT5 regulates stem cells in breast cancer and leukemia are different.

Surprisingly, none of our top differentially expressed validated genes appeared to have a close correlation with breast cancer pathogenesis (Figures S5B and S5C), and although CDKN1A was validated as a PRMT5-repressed gene (Figure S6B), the functional significance of this is unclear given that the cell cycle profiles of shCTRL or PRMT5-depleted AR cells were indistinguishable (Figure 3F). We thus decided to focus our investigations on FOXP1, a winged helix/forkhead transcription factor that has been associated with normal and cancer stem cell function (Choi et al., 2016, Gabut et al., 2011, Naudin et al., 2017). Intriguingly, FOXP1 is generally considered a tumor suppressor in the breast because high levels correlate with better prognosis, despite the finding that it promotes proliferation and migration of breast cancer cell lines (Oskay Halacli, 2017, Shigekawa et al., 2011, Xiao et al., 2016). Because of this apparent contradiction and link with stem cell biology (Choi et al., 2016, Gabut et al., 2011), we decided to investigate the relationship between PRMT5, FOXP1, and BCSC function in more detail.

Similar to PRMT5, FOXP1 levels were significantly elevated in AR cells (Figure 6A). Importantly, expression was PRMT5 dependent, as depletion of PRMT5 decreased both protein (full-length 75 kDa FOXP1 isoform) and mRNA transcripts in AR and ESA⁺CD24^lowCD44⁺ cells (Figures 6B–6D). Moreover, FOXP1 expression was dependent on the catalytic activity of PRMT5 as reconstitution of PRMT5-depleted cells with ectopic wild-type but not catalytically inactive PRMT5 increased FOXP1 transcripts (Figure 6C). We next wanted to determine if PRMT5 was directly regulating FOXP1 expression. Using total cell population, we used chromatin immunoprecipitation (ChIP) coupled to promoter tiling to demonstrate an enrichment of PRMT5 at the FOXP1 promoter. In comparison, PRMT5 was not recruited to the MYOD1 promoter, a muscle-specific gene regulated by PRMT5 but not expressed in MCF7 cells (Dacwag et al., 2007) (Figures 6E and S7A and S7B). Importantly, PRMT5 depletion significantly reduced PRMT5 promoter occupancy (Figures 6E and S7B), confirming that PRMT5 is truly recruited to the FOXP1 promoter and validating specificity of our PRMT5 ChIP antibody. One mechanism by which PRMT5 promotes gene expression is through the methylation of H3R2 (H3R2me2s), which is recognized by WDR5, enabling the recruitment of the SET1/MLL complex and histone H3K4 trimethylation (H3K4me3) (Migliori et al., 2012). Consistent with this chain of events, H3R2me2s, SET1, and H3K4me3 were all enriched at the FOXP1 promoter in a PRMT5-dependent manner (Figures 6F–6H and S7C–S7E). Crucially, this observation was also true in the tumor-initiating population, as treatment of AR cells with the PRMT5 inhibitor GSK591 (Duncan et al., 2015) substantially reduced FOXP1 promoter H3K4me3 levels (Figure 6I), and treatment of primary mammospheres with the WDR5 antagonist OICR-9429 (Grebien et al., 2015) reduced BCSC proliferation in a dose-dependent manner (Figure S7G). Even though global levels of H3R2me2s were not altered by PRMT5 depletion (Figure S7H), our findings are highly supportive that PRMT5 is directly recruited to the FOXP1 promoter, facilitating H3K4me3 and gene expression via H3R2me2s.

Given that FOXP1 has been proposed to function as a tumor suppressor in the breast, we wanted to determine the effect of FOXP1 on MCF7 growth. In support of a pro-tumorigenic role, FOXP1 depletion in MCF7 cells results in growth suppression, whereas overexpression enhances growth (Figures 6J and 6K). More significantly, depletion of FOXP1 in xenografts significantly reduced tumor growth (Figures 6L and S7F). Indeed, transcript levels of FOXP1 are elevated >11-fold in MCF7 cells compared with immortalized but non-transformed mammary epithelial MCF10A cells (Figure 6D). Next, we wanted to determine if PRMT5-mediated upregulation of FOXP1 is required for BCSC function. Interestingly, FOXP1 depletion in MCF7 cells expressing endogenous levels of PRMT5/MEP50 reduced primary mammosphere numbers but did not significantly affect secondary mammospheres (Figures 6M and 7B), implying that under these conditions, FOXP1 regulates BCSC numbers and proliferation rather than self-renewal. In contrast, depletion of FOXP1 on the background of ectopically expressed PRMT5 and MEP50 completely abrogated the effects of PRMT5 and MEP50 overexpression on both BCSC numbers and proliferation and self-renewal (Figure 6M), implying that the effects of hyperactive PRMT5 on BCSC proliferation and self-renewal are mediated through FOXP1. These findings therefore suggest that a threshold level of FOXP1 expression, presumably via PRMT5-mediated epigenetic regulation, is required for self-renewal or that high levels of an unknown FOXP1 cofactor that drives self-renewal gene expression is present only under certain PRMT5 conditions.

Pharmacological Inhibition of PRMT5 Reduces BCSC Numbers In Vitro

Because we demonstrated that the catalytic activity of PRMT5 was required for driving BCSC function and FOXP1 expression (Figures 1G and 6C), we wanted to determine whether a small-molecule inhibitor targeting PRMT5 could affect BCSC function. We therefore treated MCF7 cells with the validated PRMT5 inhibitor GSK3203591 (EPZ015866; herein referred to as GSK591) (Figure 7A; Duncan et al., 2015). Similar to PRMT5 depletion, inhibition of PRMT5 significantly suppressed MCF7-derived BCSC proliferation and self-renewal and the number of ALDEFLUOR⁺ T47D cells (Figures 7B and S7I), while overexpression of FOXP1 was able to rescue the BCSC proliferative defect induced by GSK591 (Figure 7C). Our data thus imply that drug targeting PRMT5 reduces the activity of BCSCs, but given that depletion of FOXP1 and GSK591 was not epistatic in reducing primary and secondary mammospheres (Figure 7B), FOXP1 is important but not sufficient for all PRMT5-dependent events in BCSCs.

PRMT5 has been reported as a critical component of normal stem cell function (Chittka et al., 2012, Liu et al., 2015), hence one potential limitation of PRMT5-directed therapies for breast cancer is the suppression of normal mammary stem cell function. Interestingly, although knockdown and inhibition of PRMT5 reduces the number of primary mammospheres of MCF10A cells, self-renewal was unaffected (Figures 7B, S7I, and S7J). In support, stem cell numbers, as determined by ALDEFLUOR staining was unaffected by GSK591 (Figure S7I). Moreover, this lack of effect of PRMT5 deletion or inhibition on MCF10A self-renewal was not due to receptor status, as treatment of the triple-negative breast cancer cells SUM159 with GSK591 phenocopies that of MCF7 cells, reducing both BCSC proliferation and self-renewal (Figure 7B). Hence, it appears that PRMT5 activity specifically affects self-renewal of cancer rather than normal mammary stem cells.

We next wanted to evaluate the ability of PRMT5 depletion to synergize with conventional chemotherapy for ER⁺ tumors. Although PRMT5 depletion did not alter the ability of 4-hydroxytamoxifen (4-OHT), the active metabolite of tamoxifen, to suppress primary mammosphere numbers (Figure 7D), secondary mammosphere formation was markedly reduced (Figure 7E). Thus, PRMT5 inhibitors in combination with 4-OHT appear to synergistically suppress BCSC self-renewal.

To correlate our cell culture findings with therapeutic potential, we isolated cancer cells from freshly resected ER⁺ patient-derived tumors from a cohort that had not undergone neo-adjuvant chemotherapy and conducted mammosphere analysis in the presence of GSK591. Continuous treatment of patient-derived BCSCs with GSK591 markedly suppressed mammosphere formation, indicative that inhibition of PRMT5 is effectively depleting primary-derived BCSCs (Figure 7F). Taken together, our results strongly imply that therapeutic targeting of PRMT5 could be an effective way of eradicating the cancer stem cell compartment.

Isolation of Stem Cell-Enriched Populations

BCSCs were isolated by either flow cytometry sorting of ESA⁺CD24^lowCD44⁺ MCF7 cells or by isolation of AR cells using the Miltenyi Dead Cell Removal kit. For further details, see Supplemental Experimental Procedures.

Generation of Stable Cell Lines

Cell lines stably expressing shRNA sequences were generated by transducing with lentiviral supernatant containing 8 μg/mL polybrene (Sigma-Aldrich) by centrifugation for 90 min at 4,000 rpm. See Supplemental Experimental Procedures for more details and shRNA sequences.

Mammosphere Assay

MCF7, T47D, and MCF10A cells were plated onto pHEMA (Sigma-Aldrich)-coated six-well plates and cultured at 37°C for 5 days. Mammospheres >50 μm were scored using a graticle. For serial replating, mammospheres were disaggregated and cultured for a further 5 days prior to scoring. For drug treatment, cells were incubated with 5 μM GSK591 or 2.5 μM 4-OHT (Sigma-Aldrich) or vehicle controls. For further details, see Supplemental Experimental Procedures.

Xenograft Studies and In Vivo Imaging

Animal experiments were conducted in accordance with United Kingdom Home Office regulations. For the limiting dilution assay, 5- to 7-week-old female NSG mice were injected with the appropriate number of cells and a slow release estrogen pellet (NE-121; Innovative Research of America) was subcutaneously implanted at the base of the tail. Two hours prior to harvest at the experimental endpoint, mice were injected with 100 mg/kg BrdU (Sigma-Aldrich). For in vivo depletion of PRMT5, female NSG mice were injected with 5 × 10⁶ cells and once tumors were palpable, maintained on a diet of dox chow (T-5BQ8-1816629-203; TestDiet). For imaging, mice were injected intraperitoneally (i.p.) with 150 mg/kg of luciferin (Promega), and images were captured on an IVIS Spectrum. See Supplemental Experimental Procedures for more detail.

RNA Sequencing

Three independent replicates of ESA⁺CD24^lowCD44⁺ cells were isolated by flow cytometry from MCF7 shCTRL or shPRMT5 cells. Total RNA was extracted and rRNA was depleted prior to sequencing on the Illumina Hiseq. Sequenced reads were mapped to build hg19 of the human genome from the University of California, Santa Cruz (UCSC) genome database. Differential gene expression was determined using Cuffdiff 2.2.1 with a threshold of false discovery rate (FDR) <0.05 and fold change >1.5. Enriched Gene Ontology terms and KEGG pathways were identified using DAVID (https://david.ncifcrf.gov) (Huang et al., 2009). For more detail, see Supplemental Experimental Procedures.

ChIP

Chromatin extraction and ChIP were performed as described previously (Clarke et al., 2017). Briefly, cells were fixed, lysed, and sonicated to produce DNA fragments of between 300 and 500 bp. Chromatin was precleared and ChIP was performed using chromatin equivalent to 5 × 10⁶ cells. Chromatin was incubated overnight at 4°C with antibody followed by 3 hr incubation with protein G beads. Immunoprecipitated DNA was reverse crosslinked and treated with proteinase-K. DNA was isolated by phenol/chloroform extraction and ethanol precipitation. For ChIP of AR cells, cells were treated for 5 days with 5 μM GSK591 prior to replating overnight in suspension. AR cells were isolated using the Miltenyi Dead Cell Removal kit. Following isolation, cells were processed as above. For more detail, see Supplemental Experimental Procedures.

Statistical Analysis

Unless otherwise stated, error bars represent mean ± SEM, n ≥ 3 animals or experimental repeats. All statistical analysis was carried out using Student’s t test (^∗p < 0.05, ^∗∗p < 0.001, ^∗∗∗ p < 0.005).