Elevated FOXG1 supports exit from quiescence in neural stem cells through FoxO6

  1. Kirsty M Ferguson
  2. Carla Blin
  3. Claudia Garcia-Diaz
  4. Harry Bulstrode
  5. Raul Bardini Bressan
  6. Katrina McCarten
  7. Steven M. Pollard

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Abstract

The molecular mechanisms controlling the balance of quiescence and proliferation in adult neural stem cells (NSCs) are often deregulated in brain cancers such as glioblastoma (GBM). Previously, we reported that FOXG1, a forebrain-restricted neurodevelopmental transcription factor, is frequently upregulated in glioblastoma stem cells (GSCs) and limits the effects of cytostatic pathways, in part by repression of the tumour suppressor Foxo3 . Here, we show that increased FOXG1 upregulates FoxO6 , a more recently discovered FoxO family member with potential oncogenic functions. Although genetic ablation of FoxO6 in proliferating NSCs has no effect on the cell cycle or entry into quiescence, we find that FoxO6 -null NSCs can no longer efficiently exit quiescence following FOXG1 elevation. Increased FoxO6 results in the formation of large acidic vacuoles, reminiscent of Pak1-regulated macropinocytosis. Consistently, Pak1 expression is upregulated by FOXG1 overexpression and downregulated upon FoxO6 loss in proliferative NSCs. These data suggest a pro-oncogenic role for FoxO6 in controlling the exit from quiescence in NSCs, and shed light on the functions of this underexplored FoxO family member.

Research highlights

  • FoxO6 is a downstream effector of elevated FOXG1 in mouse NSCs and GSCs.

  • Upregulation of FoxO6 is necessary for FOXG1 to drive efficient quiescence exit of NSCs.

  • FoxO6 overexpression stimulates macropinocytosis, a process regulated by the actin cytoskeleton regulator Pak1.

  • Pak1 is upregulated by FOXG1 overexpression and downregulated upon FoxO6 loss.

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    Reviewer #1 (Evidence, reproducibility and clarity (Required):

    The majority of the conclusions are well supported by strong experimental evidence. The only area where that is not fully the case is the role of Pak1 as a downstream effector of FoxG1-FoxO6 and its effects on macropinocytosis. To further strengthen this claim, the authors should demonstrate that ablation of Pak1 can rescue the functional consequences of forced FoxO6 expression and whether overexpression of Pak1 rescues quiescence exit in FoxO6 knockout. Thank you to the reviewer for these helpful suggestions. To investigate the effects of Pak1 ablation, and therefore more directly the link between FOXG1 and FoxO6 and macropinocytosis, we tested the published Pak1 inhibitor IPA-3. Unfortunately, to distinguish the role of Pak1 in quiescence exit and macropinocytosis, we would need a dosage of IPA-3 that is efficacious but does not affect cell proliferation. It was not possible to optimise such a dosage (a dosage of 10uM is shown to be efficacious at inhibiting Pak1 (Verma et al, 2020; Wong et al, 2013) however even at 2.5uM we see significant cell death in our cells. Indeed, this is potentially due to pleiotropic roles for Pak1.

    Also, it is not feasible to overexpress Pak1 in the FoxO6 KO cells with inducible FOXG1. To ensure we are investigating quiescence exit this would need to be in an inducible manner; however, re-transfecting cells using the PiggyBac system would potentially alter FOXG1 transgene levels by excising the existing transgene.

    As shown in Figure S3, we do not observe clear vacuole formation in F6 (FOXG1-inducible) cells upon Dox addition. As detailed in the discussion, we hypothesise that FoxO6-induced macropinocytosis could represent a stalled state, with other pathways downstream of FOXG1 necessary to be activated concomitantly to ensure cell cycle re-entry, e.g., through increased pinocytic flux that cannot be assessed within our experimental timeframes. Indeed, active Pak1 has been found to modulate pinocytic cycling, enhancing both FITC-dextran uptake and efflux (Dharmawardhane et al, 2000). We therefore would not hypothesise that high Pak1 levels alone would be sufficient to drive quiescence exit.

    Alternatively, the macropinocytosis observed may be a metabolic stress response because of the hyperactivation of signalling pathways upon FoxO6 overexpression. Hyperactivation of Ras signalling, canonical Wnt and PI3K signalling have all been shown to play roles in inducing macropinocytosis (Overmeyer et al, 2008; Tejeda-Muñoz et al, 2019; Recouvreux & Commisso, 2017).

    We believe the observed macropinocytosis phenotype upon Foxo6 overexpression, and the changes in Pak1 expression upon Foxo6 loss or FOXG1 induction provide interesting insights into the function of this underexplored FoxO family member. However, currently we are unable to demonstrate a direct link between these processes and have therefore modified the text to reflect this (see lines 292-4, 330-3, 365-8).

    • The manuscript stresses the role of NSC quiescence exit in GBM and demonstrates that FoxG1 KO reduces FoxO6 levels in a murine GBM cell line but a BMP4-mediated quiescence and dox-induced FoxG1 over-expression or an abolishment of cell cycle re-entry thereof by reduced FoxO6 levels in the case of FoxG1 KO is lacking. But this would significantly substantiate the relevance of the findings. *

    Mouse GBM cells have elevated levels of FoxG1 and have been shown to be refractory to BMP4-mediated quiescence entry, maintaining colony formation following BMP treatment (Bulstrode et al, 2017). It is therefore challenging to specifically investigate cell cycle re-entry/ quiescence exit using these mouse GBM cells, or indeed any GBM cell line due to their inability to respond fully to BMP cues (Caren et al, 2015). It has also been shown by Bulstrode et al, 2017 that Foxg1 null mouse neural stem cells show an increased propensity to exit cycle in response to BMP treatment, and reduced colony formation on return to EGF/FGF-2 growth factors. FOXG1 null cell lines therefore show a reduced response to BMP cues, making it difficult to explore quiescence exit per se.To navigate this, instead we investigated Dox-induced FOXG1 overexpression in FoxO6 WT and KO mouse NS cells, which display similar quiescence characteristics upon BMP treatment (Figure 4).

    • In the introduction and discussion, FoxO6 is mentioned for its oncogenic roles in various cancers but no reference to GBM specifically is cited. It feels like a missed opportunity to not show evidence of this in the IENS cell line that has reduced levels of FoxO6; is there an effect in their proliferative capacity? What are the expression levels of Pak1 following FoxG1 KO in IENS cells? *

    Thank you for the helpful suggestion. It is indeed true the literature on FoxO6 in GBM is lacking, explaining the absence of citations on this. On investigation of expression of the proliferation marker Ki67 in these cells we found no significant difference in expression, now shown in Figure 1H. This is in fitting with previous findings of our lab (Bulstrode et al, 2017) which show that FOXG1 is dispensable for the maintenance of continued NSC or GSC proliferation in vitro. We investigated the expression levels of Pak1 following FOXG1 KO in IENS and found a decrease in both KO lines compared to parental cells (updated Figure 6F).

    As explained in our discussion, these data suggest that Foxg1/FoxO6/Pak1 are not functionally important in sustaining GSC/NSC proliferation, as shown by the lack of proliferation defects upon Foxg1 or FoxO6 deletion (Bulstrode et al, 2017), but impact regulatory transitions, as cells prepare to exit quiescence into the proliferative radial-glia like state.

    *Minor comments *

    - Fig1A shows 4 and 2-fold respectively for the two mouse NSC lines, not 17 and 4-fold increase as written on manuscript, please adjust accordingly.

    The qRT-PCR data are presented as log2(fold change) or - ddCt, where this value equals zero for the calibrator sample, as indicated in the figure legends and axes. The data are presented in this way to enable accurate visualisation of up- and down-regulation of gene expression. Data are stated as ‘fold increase’ in the text for ease of reading, which we have clarified in the text and figure legends (e.g. lines 154 and 176).

      • Fig2G manuscript reports a 235-fold upregulation, but graph looks more like a 7 or 8-fold as shown on Fig1A for the F6 NSC line. I would recommend checking the fold changes reported throughout the paper. *

    See previous comment above. The qRT-PCR data are presented as log2(fold change) or - ddCt, where this value equals zero for the calibrator, as indicated in the figure legends and axes. The data are presented in this way to enable accurate visualisation of up- and down-regulation of gene expression. Data are stated as ‘fold increase’ in the text for ease of reading, which we have clarified in the text and figure legends (e.g. lines 154 and 176).

    • The manuscript describes the increase of FOXG1 after BMP4-induced cell cycle exit as compared to non-BMP4 treated cells (p.8 first paragraph), but I am wondering if this expression is rather compared to dox negative and not vs BMP4 negative treatment. *

    Data are presented relative to the non-BMP treated (EGF/FGF-2) control throughout the manuscript for consistency. This is to enable changes in expression between -Dox and +Dox to be visualised throughout the quiescence-exit time course relative to the initial starting population in EGF/FGF-2 growth media, prior to BMP treatment.

    •  7.  In Fig2G it is interesting that FoxO6 is upregulated in BMP4 treated throughout the experiment with highest values at day10 post treatment. At the same time, non-BMP4 treated cells keep decreasing their FoxO6 levels dramatically but there is no mention or reference to this effect.*

    In Figure 2G, all cells have been treated with BMP4, prior to return to growth media (EGF/FGF) with or without Dox. It is true that in the +Dox condition with FOXG1 induction, FoxO6 levels continue to increase up to Day 10, perhaps reflective of the expansion of a highly proliferative radial glia-like population.

      1. Fig2 would benefit from a western blot like Fig1D where FoxG1 and FoxO6-HA protein levels are also shown in dox-treated comparing BMP4-treated vs non-treated. *

    Due to the lack of specific FoxO6 antibodies and the absence of a FoxO6-HA tag in this cell line, it is not possible to perform protein analysis of FoxO6 levels in this figure as for Figure 1D.

    • The colonies in Fig3E should be quantified, as their ability to form neurospheres seems somewhat compromised upon FoxO6 KO. Fig3B and 3F could perhaps be consolidated into one panel in the interest of space and presentation. *

    Good suggestion. We have now consolidated Fig 3B and 3F into one panel (now Figure 3F) as suggested by the reviewer. We performed additional replicates for Figure 3E to quantify the colony formation efficiency. This showed a small but insignificant decrease in colony forming ability in the KO cells (Figure 3E). Importantly the FoxO6 null cells do form colonies, and our results show that FoxO6 is not essential for proliferation or colony formation of NSCs in EGF/FGF-2 – this therefore does not account for the complete loss in colony formation we see the in the FoxO6 KO cells upon FOXG1 induction.

    • Fig4A shows vs "parental" non-BMP on y axis but wouldn't this show fold change of dox+ parental vs parental. The authors should clarify this. *

    All samples in Figure 4A are compared to parental cells in EGF/FGF-2, i.e. non-BMP treated, as the calibrator sample where log2(fold change) equals zero. We chose to set a single calibrator sample for all data (parental and FoxO6 KO cells included) to allow us to compare changes in FOXG1 transgene across the entire experiment.

    • Perhaps the authors can add a non-BMP4 treated count of % FOXG1 positive cells to Fig4C for reference. *

    As shown in Figure 4A, both parental and FoxO6 KO cells show similar, i.e. negligible, FOXG1 transgene expression without Dox, compared to the parental non-BMP4 treated control, therefore negligible FOXG1-V5 positive cells are seen by ICC. We have edited Figure 4A to include a non-BMP treated and BMP-treated control to show the negligible FOXG1-V5 expression by qPCR as controls.

    • The sentence mentioning Fig5D for the first time (p.10 third paragraph) needs rephrasing for clarity and should also call out Fig5C for the mCherry expression live cell imaging data where appropriate. Fig5D does not appear to be live imaging as implied by the text. If vacuole formation is observed already as early as 10-11h after Dox induction, then it should be shown somewhere in Fig5. Vacuole formation is shown with a higher magnification image inset only in the 22h timepoint image. I think Fig5E should be more substantiated with some sort of quantification, e.g. % of vacuoles positive for EEA1 and/or LAMP1. *

    We apologise for this. The first reference to Figure 5D one line 234 should refer to Figure 5C, this has now been corrected in the text. Vacuoles are visible in Figure 5C panel 10 h 30 min, however, to make this clearer we have also supplied an accompanying movie of the live imaging (Movie 1). The imaging in Fig 5E has not been quantified as this imaging was performed with the purpose of confirming the vacuole structures seen are not simply enlarged lysosomes, due to their similarity in appearance to those published elsewhere (Ramosaj et al, 2021; Leeman et al, 2018). Instead, we have provided Western blotting data in Figure S5E to support this conclusion that there is no clear increase in EEA1 or LAMP1 (early endosomal or lysosomal) expression upon FoxO6-HA induction.

    *- Could the authors comment on the lack of proliferative advantage of the FoxO6 overexpression. FigS3 shows Edu staining, but there is no proliferation assay in either Fig5 or S3. What would be the effect of FoxO6 overexpression on BMP4-mediated quiescence with or without FoxG1 over-expression? *

    Induction of FoxO6-HA overexpression does not provide a proliferative advantage to the cells. Looking at individual cells, those with high FoxO6-HA levels seem to associate with EdU negativity. In Figure S3 we provide quantitative EdU incorporation assay as a proliferation assay (quantification of the number of cells cycling, therefore incorporating EdU, within a 24h pulse period). Quantification of the EdU staining in Figure S3G is provided in Figure S3H. We have now clarified this in the text on page 11, lines 263-4.

    Unfortunately, due to transgene overexpression using the PiggyBac transposon method, it is not feasible to overexpress FoxO6 and FOXG1 in the same cell line, as re-transfecting cells using the PiggyBac system would potentially alter FOXG1 transgene levels and make results difficult to interpret. Given the association of vacuolated cells with EdU negativity, we predict that FoxO6 overexpression would not give an advantage for quiescence exit. Indeed, BMP-treated cells with FoxO6 overexpression show a decrease in EdU positivity, as shown in Figure S3H. As discussed in the text, we hypothesise that cells with FoxO6 overexpression are in a stalled state, potentially due to signalling hyperactivation. While this may not be physiological, it gives us clues as to the function and downstream targets of FoxO6, which remain uncharacterised.

    *- Can the authors clarify if there is a proliferation change in F6 cells in Fig6F as in Fig2F? Fig6F shows Pak1 is already upregulated in quiescent NSCs, what are the expression levels of Pak1 in FoxO6 -/- ANS4 cells upon FoxG1-mediated quiescence exit as shown in Fig4? Is there a particular reason why the F6 cell line data is shown only up to day2 post Dox-induction rather than d4 or d10? For consistency with the rest of similar experimental data this timeline should be extended. Does Pak1 remain elevated, plateaus or keeps reducing further post day2? *

    The data is (previous) Figure 6F is the same assay and cell line as presented in Figure 2, but at an early timepoint (Day 2) during the quiescence exit assay. We have provided in the panel qRT-PCR analysis of Ki67 to show that cells begin to show increased proliferation at this timepoint. Due to our hypothesis that Pak1 is required at an early transition point, we decided to analyse this expression at an earlier timepoint than Figure 2. We have also repeated this at D10 (data below), showing Pak1 levels continue to increase with time, along with FoxO6 and the proliferative marker Ki67. Due to technical issues with variable FOXG1 transgene levels we were unable to analyse Pak1 expression levels in FoxO6+/- ANS4 cells upon FOXG1-mediated quiescence exit.

    *15 . Reviewer #1 (Significance (Required)): *

    The study provides a conceptual advance for exit from stem cell quiescence. There is strong evidence provided for murine neural stem cells, but the link to GBM cancer stem cells is less developed (but perhaps this is the subject of a separate manuscript).

    *While FoxG1 is a known regulator of neurodevelopment and glioblastoma, the functions of FoxO6 have not been studied in the context of neural stem cells. In my view, this study should be of high interest to audiences in both neurodevelopment and cancer research. * *Expertise: glioblastoma, cancer stem cells, neurodevelopment *

    We have edited the text and title to clarify that neural stem cells are used here as a model for GSCs with high levels of FOXG1 (e.g. lines 36 and 69).

    Reviewer #2 (Evidence, reproducibility and clarity (Required)):

    *Major comments: *

    *-The choice of NSCs as a main experimental model to understand the effects of FoxG1 and FoxO6 is not fully justified. The authors had previously shown that FoxG1 is expressed at very low levels in NSCs (Fig. 1A in Bulstrode et al. 2017). FoxO6 also seems to be barely expressed in NSCs (Fig. 1 of the current manuscript) and, in addition, its levels seem to go further down as cells exit quiescence (-Dox line in Fig. 2H). Therefore, these two genes do not seem to play an important role in the normal exit from quiescence of NSCs, with FoxO6 only affecting FoxG1 overexpression-induced exit from quiescence. *

    • **If the aim is to mimic a GBM-like state by FoxG1 overexpression, this should be made much clearer in the text, including title and abstract. In that case, the authors should also show a direct comparison of the levels of FoxG1 in GBM and upon Dox-induced overexpression in NSCs. *

    We agree with this criticism and suggestion to fix this. It is indeed our aim to mimic a GBM-like state by inducing FOXG1 overexpression and we should have made that more explicit. All experiments are performed in the context of high FOXG1 level. Like Foxg1, FoxO6’s homeostatic roles may be subtle in adulthood, and mostly involved in neural plasticity (Yu et al, 2019). This is in keeping with our finding that basal FoxO6 levels are low in adult NSCs and not required for sustained proliferation but are important for cell state transitions. If the FoxO6 levels activated by elevated FOXG1 represent an acquired dependency of GBM, there may be a therapeutic window to target this pathway. However, given the poorly understood roles of FoxO6, further work is needed to determine its specific value as a therapeutic target. We have modified the title and the text to make this clearer. This is also stated in the first paragraph of the results section on page 7 (line 148).

    We have provided below a Western Blot (Bulstrode, 2016) in which FOXG1 levels in F6 cells induced with Dox (1000 ng/ml the dosage used) with the GBM cell lines G7 and G144, and the normal NS cell line U5. This shows that the FOXG1 levels induced are significantly higher than found in normal neural stem cells (mouse or human). This model has been previously used and published in Bulstrode et al, 2017, upon which this manuscript expands.

    *-While the authors state that they aim to study NSC quiescence, they use a protocol that is closer to modelling astrocytic differentiation. In fact, in their previous work, they use this very same protocol (removal of growth factors and addition of BMP) to study the role of FoxG1 and Sox2 on astrocyte de-differentiation (Bulstrode et al. 2017). While there is arguably no perfect in vitro model of NSC quiescence, the current standard in the field is treatment with both BMP and FGF for 48 to 72 hours (e.g.: Mira et al., 2010, Martynoga et al., 2013, Knobloch et al., 2017, Leeman et al., 2020). BMP alone is regarded as a pro-astrocytic differentiation cue, and 24 hours might not be enough for NSCs to fully commit to either differentiation or quiescence. Therefore, either the claims in the paper are changed to match the astrocytic differentiation model, or a standard quiescence protocol should be used throughout to confirm the findings also apply to the exit from quiescence of NSCs. *

    We agree with the reviewer that there is indeed no perfect* in vitro *model of NSC quiescence and thank the reviewer for this useful discussion. Coincident with this project, this was an active area of research from our laboratory as explored by Marques-Torrejon et al, 2021 (Nature Comms). After 24 h BMP4 treatment, we found that adult mouse NS cells: exit cell cycle, are growth factor unresponsive, obtain an astrocytic morphology, upregulate astrocytic markers such as Gfap and Aqp4, and downregulate radial glia/NS cell markers such as Nestin and Olig2 (Figure 3).

    We therefore initially viewed them as terminally differentiated. However, the exact state of these cells is difficult to define due to the lack of definitive markers and transcriptional differences that can distinguish terminally differentiated GFAP-expressing astrocytes from quiescent type B SVZ NS cells (which also express GFAP) (Bulstrode et al, 2017; Doetsch et al, 1999; Codega et al, 2014). Findings from our laboratory later suggested some NS cell markers are maintained following BMP4 treatment and these cells can be forced back into cycle with combined Wnt/EGF signalling, or FGF/BMP signalling (Marques-Torrejon et al 2021). This suggests* in vitro* NS cells may lie along a continuous spectrum of states from dormant quiescent, activated quiescent (primed for cell cycle re-entry) to actively proliferating, similar to that observed in vivo in the mouse SVZ (Dulken et al, 2017). Indeed, after 24 h BMP4 treatment, we observe a minimal level of colony formation in no Dox controls following 10 days of exposure to the growth factors EGF/FGF-2 (Figure 2D-F).

    These non-cycling BMP4-induced astrocytic cells might therefore be better viewed as dormant quiescent NSCs, hence our reference as quiescent NSCs. The assay conditions used in this manuscript differ to those of Marques-Torrejon et al, in terms of density and length of BMP4 treatment; it is therefore likely that our BMP-treated cells are at different stages along the continuum between dormancy and primed quiescent states. Importantly, regardless of the exact cell type induced by 24 h BMP4 treatment, we have considered the changes induced by FOXG1 overexpression, in comparison to the effect of NS cell media alone.

    *-The FoxO6-induced vacuole formation in NSCs is a very interesting finding. However, so far it was only observed upon FoxO6 overexpression. To claim vacuolization is required for quiescence exit, the authors should show whether this phenomenon is also observed upon normal exit from quiescence and FoxG1-induced reactivation of NSCs. From the author's own data, Pak1 (which induces vacuolization) is unlikely to reactivate NSCs, as its expression is highest in BMP-treated cells (Figure 6F). The authors should show whether some vacuolization is present at these stage in NSCs and if not, discuss the possible interplay between Pak1 and FoxO6 in vacuole formation and quiescence exit. *

    As detailed in the discussion, we hypothesise that FoxO6- induced macropinocytosis could represent a stalled state, with other pathways downstream of FOXG1 necessary to be activated concomitantly to ensure cell cycle re-entry, e.g., through increased pinocytic flux that cannot be assessed within our experimental timeframes. Indeed, active Pak1 has been found to modulate pinocytic cycling, enhancing both FITC-dextran uptake and efflux (Dharmawardhane et al, 2000). Alternatively, the macropinocytosis observed may be a metabolic stress response because of hyperactivation of signalling pathways upon FoxO6 overexpression Hyperactivation of Ras signalling, canonical Wnt and PI3K signalling have all been shown to play roles in inducing macropinocytosis (Overmeyer et al, 2008; Tejeda-Muñoz et al, 2019; Recouvreux & Commisso, 2017).

    We do not see clear evidence of vacuoles in FOXG1-induced reactivation of NSCs – this supports that the macropinocytosis seen upon FoxO6 overexpression is a stalled state or due to hyperactivation. While this may not be physical, it gives us clues as to the function and downstream targets of FoxO6, which remain uncharacterised (such as a link of FoxO6 and FOXG1 with Pak1-related pathways). Demonstrating a requirement for vacuolisation in quiescence exit is outwidth this manuscript and therefore we are careful not to claim this. We have modified the text to clarify this.

    As the reviewer noted, it is interesting that Pak1 is highest in BMP-treated cells; it seems that BMP signalling itself is triggering elevated Pak1 levels, likely as cells undergo extensive cell shape changes during the transition from proliferation to quiescence. However, in EGF/FGF-2, Pak1 levels decrease, and our data suggests that FOXG1/FoxO6 are required to increase or maintain Pak1, potentially to again enable the cell shape/metabolic changes required on quiescence exit. We have added to the text to expand upon this observation on page 14 (lines 330-333). -Finally, the data on the regulation of Pak1 expression by FoxO6 is insufficient to draw any strong conclusions. Downregulation of Pak1 in FoxO6 cells is not enough evidence to claim a direct regulation. The authors should show whether Pak1 levels are increased after FoxO6 overexpression and whether FoxG1 is downregulated in FoxO6 KO NSCs (indirectly affecting Pak1 expression).

    We have performed qRT-PCR analysis of Foxg1 expression in FoxO6 KO NSCs and see no consistent difference in expression, indicating this is not indirectly affecting Pak1 expression (see below, 1). We have also investigated Pak1 levels upon FoxO6 overexpression, over a time course following Dox addition (see below, 2). Interestingly, when FoxO6 is overexpressed, Pak1 is not clearly upregulated at any time-point. It may be that as Pak1 is already expressed in the -Dox controls, due to its roles in a variety of cellular functions, that the levels are saturated already. It is clear that Pak1 expression decreases upon FoxO6 loss in EGF/FGF (without coincident Foxg1 downregulation) and in F6 cells, higher FOXG1 correlates with higher Pak1 in EGF/FGF. Together with the induction of macropinocytosis upon FoxO6 overexpression, these data provide interesting insights into the potential pathways downstream of Foxo6 in controlling quiescence exit, directly or indirectly related to Pak1 signalling. We have modified the text to reflect this on page 14 (lines 330-333).

    *Minor comments: * *Please state in the main text that NSCs are derived from the SVZ. *

    This has been added to the text on page 7 (line 149) and is in the methods ‘Cell Culture’ section.

    Reviewer #2 (Significance (Required)):

    As I said before, I find this work tackles a very important question, how is the exit from quiescence controlled in NSCs. This manuscript will be of interest to researchers in the fields of adult stem cell biology and adult neurogenesis. While my expertise lies mostly on NSC biology, this work is of potential great interest for the cancer field, particularly for brain cancer research. Elucidating the mechanisms GBM cells use to exit quiescence is crucial in order to avoid the relapse of this aggressive form of brain cancer. To increase the relevance of the work to the cancer community, some of the key findings should be reproduced with GBM cells. It would be particularly important to show whether Pak1 induced vacuolization and macropinocytosis can be observed in GBM cells.

    As detailed in the discussion, we hypothesise that FoxO6- induced macropinocytosis could represent a stalled state, with other pathways downstream of FOXG1 necessary to be activated concomitantly to ensure cell cycle re-entry, e.g., through increased pinocytic flux that cannot be assessed within our experimental timeframes. Alternatively, the macropinocytosis observed may be a metabolic stress response because of hyperactivation of signalling pathways upon FoxO6 overexpression Hyperactivation of Ras signalling, canonical Wnt and PI3K signalling have all been shown to play roles in inducing macropinocytosis (Overmeyer et al, 2008; Tejeda-Muñoz et al, 2019; Recouvreux & Commisso, 2017). We do not see clear evidence of vacuoles in FOXG1-indued reactivation of NSCs– this supports that the macropinocytosis seen upon FoxO6 overexpression is a stalled state or due to hyperactivation. We do not therefore think macropinocytosis per se would be observed in quiescence exit of GBM cells – indeed a normal form of macropinocytosis-induced cell death called methuosis has been observed in GBM cells with hyperactivated Ras signalling (Overmeyer et al, 2008). However, this phenotype still gives us clues as to the function of FoxO6 in quiescence exit in GSCs and the downstream signalling pathways it may regulate, such as Pak1-related signalling (discussed on lines 330-3 and 366-9).

    Reviewer #3 (Evidence, reproducibility and clarity (Required)):

    *Summary: * *The overall objective of the paper is to investigate the mechanisms by which co-option of the activity of developmental master lineage regulators by cancer cells allows them to gain fitness. To answer this question, they focus on FOXG1. This TF acts during the specification of the telecephalon. Its expression can be increased in Glioblastoma (GBM) and, more importantly for the paper, FOXG1 has previously been shown to promote exit from quiescence of glioblastoma stem cells (GSCs) and non-transformed neural stem cells (NSCs). In a previous screen, the authors identified FoxO6 as a potential direct target gene of FOXG1. In this paper, they showed that with the gain of expression for FOXG1 in NSCs and loss of FOXG1 in GSCs, FoxO6 is increased or decreased, respectively. Loss of FoxO6 in NSCs does not alter their cell cycle or cell shape and specification. Yet, loss of FoxO6 in NSCs blocks FOXG1-mediated exit from quiescence. To understand the mechanisms, they decided to overexpress FoxO6 in NSCs and demonstrated that the cells undergo macropinocytosis, a process by which cells can engulf large amount of nutriments from the external medium. It remains to be determined whether this macropinocytosis occurs in cells overexpressing FOXG1 and GSCs. The authors provide a first answer by showing that overexpression of FOXG1 induces not only FoxO6 but also the expression of PAK1, one of the key kinases that regulates the membrane engulfment of macropinocytosis in NSCs. In GSC lines, the decrease of FOXO6 decreases PAK1 levels. *

    *Major comments: * *The paper describes interesting and convincing results (number of cell lines, repeated experiments seems sufficient) but it is difficult to reconcile them all in a single model, and this diminishes the impact of the study. Epistatic interactions between FoxG1, FoxO6, PAK1 and macropinocytosis are not always studied in the same cell models. Whether FOXG1-induced exit from quiescence of NSCs is dependent on a FOXG1-->FOXO6-->PAK1-->Macropinocytosis axis remains to be demonstrated. Also does such an axis operate in tumor cells remains to be fully assessed? In particular, if FoxO6 overexpression in NSCs can induce macropinocytosis, is this cellular process induced by FoxO6 downstream of FOXG1 activity during NSC quiescence exit? Is PAK1 a relay of FoxO6? Experiments looking at macropinocytosis and the involvement of PAK1 in the cell models of Figure 4 will definitely help to bridge the different results all together. *

    We thank the reviewer for this useful insight and discussion for future work.

    To directly investigate the effects of Pak1 ablation, and therefore more directly the link between FOXG1 and FoxO6 and macropinocytosis, we tested the published Pak1 inhibitor IPA-3. Unfortunately, to distinguish the role of Pak1 in quiescence exit and macropinocytosis, we would need a dosage of IPA-3 that is efficacious but does not affect cell proliferation. It was not possible to optimise such a dosage (a dosage of 10uM is shown to be efficacious at inhibiting Pak1 (Verma et al, 2020; Wong et al, 2013) however even at 2.5uM we see significant cell death in our cells. Indeed, this is potentially due to the variety of cellular functions Pak1 is involved in. Conversely, it is not feasible to overexpress Pak1 in the FoxO6 KO cells with inducible FOXG1. To ensure we are investigating quiescence exit this would need to be in an inducible manner; however, re-transfecting cells using the PiggyBac system would potentially alter FOXG1 transgene levels (through excision of the existing transgene) and therefore make results difficult to interpret.

    We hypothesise that FoxO6- induced macropinocytosis could represent a stalled state, with other pathways downstream of FOXG1 necessary to be activated concomitantly to ensure cell cycle re-entry, e.g., through increased pinocytic flux that cannot be assessed within our experimental timeframes (as detailed in the text discussion). Alternatively, the macropinocytosis observed may be a metabolic stress response because of hyperactivation of signalling pathways upon FoxO6 overexpression Hyperactivation of Ras signalling, canonical Wnt and PI3K signalling have all been shown to play roles in inducing macropinocytosis (Overmeyer et al, 2008; Tejeda-Muñoz et al, 2019; Recouvreux & Commisso, 2017). We do not see clear evidence of vacuoles in FOXG1-induced reactivation of NSCs– this supports that the macropinocytosis seen upon FoxO6 overexpression is a stalled state or due to hyperactivation and therefore not a physiological process in quiescence exit. We do not therefore think macropinocytosis per se would be observed in quiescence exit of GBM cells – indeed a normal form of macropinocytosis-induced cell death called methuosis has been observed in GBM cells with hyperactivated Ras signalling (Overmeyer et al, 2008).

    However, we believe the observed macropinocytosis phenotype upon Foxo6 overexpression, and the changes in Pak1 expression upon Foxo6 loss or FOXG1 induction provide interesting insights into the function of this underexplored FoxO family member, in GSCs and the downstream signalling pathways it may control, such as Pak1-related signalling. We have modified the text to reflect the limitations of our current data and discuss this (lines 330-3 and 366-9).

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    Referee #3

    Evidence, reproducibility and clarity

    Summary:

    The overall objective of the paper is to investigate the mechanisms by which co-option of the activity of developmental master lineage regulators by cancer cells allows them to gain fitness. To answer this question, they focus on FOXG1. This TF acts during the specification of the telecephalon. Its expression can be increased in Glioblastoma (GBM) and, more importantly for the paper, FOXG1 has previously been shown to promote exit from quiescence of glioblastoma stem cells (GSCs) and non-transformed neural stem cells (NSCs). In a previous screen, the authors identified FoxO6 as a potential direct target gene of FOXG1. In this paper, they showed that with the gain of expression for FOXG1 in NSCs and loss of FOXG1 in GSCs, FoxO6 is increased or decreased, respectively. Loss of FoxO6 in NSCs does not alter their cell cycle or cell shape and specification. Yet, loss of FoxO6 in NSCs blocks FOXG1-mediated exit from quiescence. To understand the mechanisms, they decided to overexpress FoxO6 in NSCs and demonstrated that the cells undergo macropinocytosis, a process by which cells can engulf large amount of nutriments from the external medium. It remains to be determined whether this macropinocytosis occurs in cells overexpressing FOXG1 and GSCs. The authors provide a first answer by showing that overexpression of FOXG1 induces not only FoxO6 but also the expression of PAK1, one of the key kinases that regulates the membrane engulfment of macropinocytosis in NSCs. In GSC lines, the decrease of FOXO6 decreases PAK1 levels.

    Major comments:

    The paper describes interesting and convincing results (number of cell lines, repeated experiments seems sufficient) but it is difficult to reconcile them all in a single model, and this diminishes the impact of the study. Epistatic interactions between FoxG1, FoxO6, PAK1 and macropinocytosis are not always studied in the same cell models. Whether FOXG1-induced exit from quiescence of NSCs is dependent on a FOXG1-->FOXO6-->PAK1-->Macropinocytosis axis remains to be demonstrated. Also does such an axis operate in tumor cells remains to be fully assessed? In particular, if FoxO6 overexpression in NSCs can induce macropinocytosis, is this cellular process induced by FoxO6 downstream of FOXG1 activity during NSC quiescence exit? Is PAK1 a relay of FoxO6? Experiments looking at macropinocytosis and the involvement of PAK1 in the cell models of Figure 4 will definitely help to bridge the different results all together.

    Minor comments:

    No minor comments

    Significance

    Understanding how hijacking of developmental programs by tumour cells contributes to their fitness is important for the design of cancer therapies, as these programs often confer resistance to tumour cells. Although it has been shown that FOXG1, this master TF of telencephalon specification, can give cells the ability to leave quiescence, the downstream mechanisms were unknown. The identification of FoxO6 as a relay for FOXG1 and the suggestion that this may involve macropinocytosis and the PAK1 enzyme is interesting. FoxO6 acts differently from other members of the FoxO family and PAK1 could indeed be targeted. If the authors can integrate several of their findings into a single model, their paper should be of interest to oncologists, developmental biologists and cell biologists.

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    Referee #2

    Evidence, reproducibility and clarity

    This manuscript by Ferguson et al. identifies FoxO6 as a FoxG1 target that promotes the reactivation of neural stem cells (NSCs). Quite remarkably, FoxO6 is dispensable for the proliferation or entry into quiescence of NSCs but required for their FoxG1-dependent reactivation. The authors claim that Pak1-induced macropinocytosis is required for quiescence exit and show that Pak1 expression depends on both FoxG1 and FoxO6. These findings are very interesting and could potentially help better understand the regulation of NSC quiescence. In addition, as the authors point out, they could shed light on the regulation of the exit of quiescence of glioblastoma multiforme (GBM) cells, which express higher levels of FoxG1 and FoxO6 than NSCs. The experiments are overall of high quality, with the authors making an appropriate and efficient use of CRISPR technologies to control the expression of their genes of interest in cultured NSCs. However, the findings are mostly the result of overexpression in NSCs (which do not seem to express FoxG1 or FoxO6) and the quiescence model used is neither the standard in the field nor appropriate to draw strong conclusions about quiescence exit in NSCs or GBM cells.

    Major comments:

    • The choice of NSCs as a main experimental model to understand the effects of FoxG1 and FoxO6 is not fully justified. The authors had previously shown that FoxG1 is expressed at very low levels in NSCs (Fig. 1A in Bulstrode et al. 2017). FoxO6 also seems to be barely expressed in NSCs (Fig. 1 of the current manuscript) and, in addition, its levels seem to go further down as cells exit quiescence (-Dox line in Fig. 2H). Therefore, these two genes do not seem to play an important role in the normal exit from quiescence of NSCs, with FoxO6 only affecting FoxG1 overexpression-induced exit from quiescence. If the aim is to mimic a GBM-like state by FoxG1 overexpression, this should be made much clearer in the text, including title and abstract. In that case, the authors should also show a direct comparison of the levels of FoxG1 in GBM and upon Dox-induced overexpression in NSCs.
    • While the authors state that they aim to study NSC quiescence, they use a protocol that is closer to modelling astrocytic differentiation. In fact, in their previous work, they use this very same protocol (removal of growth factors and addition of BMP) to study the role of FoxG1 and Sox2 on astrocyte de-differentiation (Bulstrode et al. 2017). While there is arguably no perfect in vitro model of NSC quiescence, the current standard in the field is treatment with both BMP and FGF for 48 to 72 hours (e.g.: Mira et al., 2010, Martynoga et al., 2013, Knobloch et al., 2017, Leeman et al., 2020). BMP alone is regarded as a pro-astrocytic differentiation cue, and 24 hours might not be enough for NSCs to fully commit to either differentiation or quiescence. Therefore, either the claims in the paper are changed to match the astrocytic differentiation model, or a standard quiescence protocol should be used throughout to confirm the findings also apply to the exit from quiescence of NSCs.
    • The FoxO6-induced vacuole formation in NSCs is a very interesting finding. However, so far it was only observed upon FoxO6 overexpression. To claim vacuolization is required for quiescence exit, the authors should show whether this phenomenon is also observed upon normal exit from quiescence and FoxG1-induced reactivation of NSCs. From the author's own data, Pak1 (which induces vacuolization) is unlikely to reactivate NSCs, as its expression is highest in BMP-treated cells (Figure 6F). The authors should show whether some vacuolization is present at these stage in NSCs and if not, discuss the possible interplay between Pak1 and FoxO6 in vacuole formation and quiescence exit.
    • Finally, the data on the regulation of Pak1 expression by FoxO6 is insufficient to draw any strong conclusions. Downregulation of Pak1 in FoxO6 cells is not enough evidence to claim a direct regulation. The authors should show whether Pak1 levels are increased after FoxO6 overexpression and whether FoxG1 is downregulated in FoxO6 KO NSCs (indirectly affecting Pak1 expression).

    Minor comments:

    Please state in the main text that NSCs are derived from the SVZ.

    Significance

    As I said before, I find this work tackles a very important question, how is the exit from quiescence controlled in NSCs. This manuscript will be of interest to researchers in the fields of adult stem cell biology and adult neurogenesis. While my expertise lies mostly on NSC biology, this work is of potential great interest for the cancer field, particularly for brain cancer research. Elucidating the mechanisms GBM cells use to exit quiescence is crucial in order to avoid the relapse of this aggressive form of brain cancer. To increase the relevance of the work to the cancer community, some of the key findings should be reproduced with GBM cells. It would be particularly important to show whether Pak1 induced vacuolization and macropinocytosis can be observed in GBM cells.

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    Referee #1

    Evidence, reproducibility and clarity

    The authors investigate mechanisms of quiescence and cell cycle entry in neural stem cells. Expanding on previous work, they show that FoxO6 is a target gene of FOXG1 in neural stem cells and glioma cancer stem cells. FoxO6 is upregulated following activation of stem cells from quiescence but is not required for proliferation. Continued over expression of FoxO6 leads to macropinocytosis through Pak1, indicating a link between FoxO6 and actin remodelling.

    Major comments

    The majority of the conclusions are well supported by strong experimental evidence. The only area where that is not fully the case is the role of Pak1 as a downstream effector of FoxG1-FoxO6 and its effects on macropinocytosis. To further strengthen this claim, the authors should demonstrate that ablation of Pak1 can rescue the functional consequences of forced FoxO6 expression and whether overexpression of Pak1 rescues quiescence exit in FoxO6 knockout.

    The manuscript stresses the role of NSC quiescence exit in GBM and demonstrates that FoxG1 KO reduces FoxO6 levels in a murine GBM cell line but a BMP4-mediated quiescence and dox-induced FoxG1 over-expression or an abolishment of cell cycle re-entry thereof by reduced FoxO6 levels in the case of FoxG1 KO is lacking. But this would significantly substantiate the relevance of the findings. In the introduction and discussion, FoxO6 is mentioned for its oncogenic roles in various cancers but no reference to GBM specifically is cited. It feels like a missed opportunity to not show evidence of this in the IENS cell line that has reduced levels of FoxO6; is there an effect in their proliferative capacity? What are the expression levels of Pak1 following FoxG1 KO in IENS cells?

    Minor comments

    • Fig1A shows 4 and 2-fold respectively for the two mouse NSC lines, not 17 and 4-fold increase as written on manuscript, please adjust accordingly.
    • Fig2G manuscript reports a 235-fold upregulation, but graph looks more like a 7 or 8-fold as shown on Fig1A for the F6 NSC line. I would recommend checking the fold changes reported throughout the paper.
    • The manuscript describes the increase of FOXG1 after BMP4-induced cell cycle exit as compared to non-BMP4 treated cells (p.8 first paragraph), but I am wondering if this expression is rather compared to dox negative and not vs BMP4 negative treatment.
    • In Fig2G it is interesting that FoxO6 is upregulated in BMP4 treated throughout the experiment with highest values at day10 post treatment. At the same time, non-BMP4 treated cells keep decreasing their FoxO6 levels dramatically but there is no mention or reference to this effect.
    • Fig2 would benefit from a western blot like Fig1D where FoxG1 and FoxO6-HA protein levels are also shown in dox-treated comparing BMP4-treated vs non-treated.
    • The colonies in Fig3E should be quantified, as their ability to form neurospheres seems somewhat compromised upon FoxO6 KO. Fig3B and 3F could perhaps be consolidated into one panel in the interest of space and presentation.
    • Fig4A shows vs "parental" non-BMP on y axis but wouldn't this show fold change of dox+ parental vs parental. The authors should clarify this.
    • Perhaps the authors can add a non-BMP4 treated count of % FOXG1 positive cells to Fig4C for reference.
    • The sentence mentioning Fig5D for the first time (p.10 third paragraph) needs rephrasing for clarity and should also call out Fig5C for the mCherry expression live cell imaging data where appropriate. Fig5D does not appear to be live imaging as implied by the text. If vacuole formation is observed already as early as 10-11h after Dox induction, then it should be shown somewhere in Fig5. Vacuole formation is shown with a higher magnification image inset only in the 22h timepoint image. I think Fig5E should be more substantiated with some sort of quantification, e.g. % of vacuoles positive for EEA1 and/or LAMP1.
    • Could the authors comment on the lack of proliferative advantage of the FoxO6 overexpression. FigS3 shows Edu staining, but there is no proliferation assay in either Fig5 or S3. What would be the effect of FoxO6 overexpression on BMP4-mediated quiescence with or without FoxG1 over-expression?
    • Can the authors clarify if there is a proliferation change in F6 cells in Fig6F as in Fig2F? Fig6F shows Pak1 is already upregulated in quiescent NSCs, what are the expression levels of Pak1 in FoxO6 -/- ANS4 cells upon FoxG1-mediated quiescence exit as shown in Fig4? Is there a particular reason why the F6 cell line data is shown only up to day2 post Dox-induction rather than d4 or d10? For consistency with the rest of similar experimental data this timeline should be extended. Does Pak1 remain elevated, plateaus or keeps reducing further post day2?

    Significance

    The study provides a conceptual advance for exit from stem cell quiescence. There is strong evidence provided for murine neural stem cells, but the link to GBM cancer stem cells is less developed (but perhaps this is the subject of a separate manuscript). While FoxG1 is a known regulator of neurodevelopment and glioblastoma, the functions of FoxO6 have not been studied in the context of neural stem cells. In my view, this study should be of high interest to audiences in both neurodevelopment and cancer research.

    Expertise: glioblastoma, cancer stem cells, neurodevelopment

  5. Version published to 10.1101/2022.06.30.498283v1 on bioRxiv