Author response:
Public Reviews:
Reviewer #1 (Public review):
Summary:
This paper seeks to understand the upstream regulation and downstream effectors of glycolysis in retinal progenitor cells, using mouse retinal explants as the main model system. The paper presents evidence that high glycolysis in retinal progenitor cells is required for their proliferation and timely differentiation into photoreceptors. Retinal glycolysis increases after the deletion of Pten. The authors suggest that high glycolysis controls cell proliferation and differentiation by promoting intracellular alkalinization, beta-catenin acetylation and stabilization, and consequent activation of the canonical Wnt pathway.
Strengths:
(1) The experiments showing that PFKFB3 overexpression is sufficient to increase the proliferation of retinal progenitors (which are already highly dividing cells) and photoreceptor differentiation are striking and the result is unanticipated. It suggests that glycolytic flux is normally limiting for proliferation in embryos.
In our BrdU birthdating experiment, we showed that PFKB3 expression drives the precocious differentiation of retinal progenitor cells (RPCs) into photoreceptors. However, we did not determine if there is an associated change in the number of dividing RPCs. To examine the proliferative status of PFKB3-overexpressing RPCs, we will perform short-term BrdU labeling to measure the number of RPCs in S-phase of the cell cycle. Additionally, we will count the number of RPCs expressing pHH3, a mitotic marker, and Ki67, a marker of cycling cells in all cell cycle phases.
(2) Likewise the result that an increase in pH from 7.4 to 8.0 is sufficient to increase proliferation implies that pH regulation may have instructive roles in setting the tempo of retinal development and embryonic cell proliferation. Similarly, the results show that acetate supplementation increases proliferation (I think this result should be moved to the main figures).
We thank the reviewer for these positive comments on our work. We will move the acetate data to the main figure as requested.
Weaknesses:
(1) Epistatic experiments to test if changes in pH mediate the effects of glycolysis on photoreceptor differentiation, or if Wnt activation is the main downstream effector of glycolysis in controlling differentiation are not presented.
Traditionally, epistasis is tested using double knock-out (DKO) studies with null mutant alleles. If two genes operate in the same pathway, the downstream phenotype prevails, whereas phenotypic worsening is observed if two genes act in parallel pathways. Our data suggests the following order of events: Pten¯®glycolysis®intracellular pH®Wnt signaling®photoreceptor differentiation. In this model, Wnt signaling is the downstream-most effector. To test our epistatic model, we will assess RPC proliferation and the differentiation of Crx+ photoreceptor precursors with the following assays:
(1) To confirm that Wnt signaling acts downstream of Pten, we will generate DKOs of Pten and Ctnnb1, a downstream effector of Wnt signaling. We know that fewer photoreceptors are generated in single Pten-cKO and Ctnnb1-cKO retinas, with a disruption of the outer nuclear layer only in Ctnnb1-cKOs. If Pten and Wnt act in the same pathway, Pten;Ctnnb1 DKOs will resemble single Ctnnb1-cKOs.
(2) While epistasis is traditionally examined using genetic mutants, we will perform proxy experiments using pharmacological agents. To test whether Wnt activation acts downstream of a pH increase, we will activate Wnt signaling with recombinant Wnt3a at high and low pH. While low pH inhibits photoreceptor differentiation, if Wnt signaling is downstream, it should promote differentiation even at low pH. Conversely, we will alter pH in the presence of a Wnt inhibitor, FH535, which should block the positive effects of high pH on photoreceptor differentiation.
(3) To test whether Wnt activation acts downstream of glycolysis to increase photoreceptor differentiation, we will apply recombinant Wnt3a to retinal explants while simultaneously inhibiting glycolysis with 2DG. While 2DG inhibits photoreceptor differentiation, if Wnt signaling is downstream, it should still be able to promote differentiation.
(4) To test whether pharmacological inhibition of Wnt signaling reverses the effects of high glycolytic activity in Pten cKO retinas, we will treat wild-type and Pten-cKO retinas with the Wnt inhibitor FH535 and/or the glycolytic inhibitor 2DG.
(2) It is likely that metabolism changes ex vivo vs in vivo, and therefore stable isotope tracing experiments in the explants may not reflect in vivo metabolism.
We agree with the reviewer that metabolism likely changes ex vivo compared to in vivo. However, we did not perform stable isotope tracing experiments to directly examine glycolytic flux in this study. While outside the scope of the current study, this type of analysis is an important future direction that we will bring up in the discussion.
(3) The retina at P0 is composed of both progenitors and differentiated cells. It is not clear if the results of the RNA-seq and metabolic analysis reflect changes in the metabolism of progenitors, or of mature cells, or changes in cell type composition rather than direct metabolic changes in a specific cell type.
We mined a scRNA-seq dataset to show that Pgk1, a rate-limiting enzyme for glycolysis, is specifically elevated in early-stage RPCs versus later stage. We have since analysed additional glycolytic pathway genes, and observed a similar enrichment of Pfkl, Eno1 and Slc16a3 transcripts in early RPCs, while other genes were equally expressed in both early and late RPCs.
To functionally demonstrate that there are differences in glycolysis between early and late RPCs, we will use CD133 to sort RPCs at E15 (early) and P0 (late). We will perform qPCR on sorted cells to validate the transcriptional differences in glycolytic gene expression. Additionally, we will perform two proxy measures of glycolysis: 1) We will measure lactate levels in sorted RPCs at both stages, and 2) We will use a Seahorse assay and assess ECAR in sorted RPCs at both stages.
(4) The biochemical links between elevated glycolysis and pH and beta-catenin stability are unclear. White et al found that higher pH decreased beta-catenin stability (JCB 217: 3965) in contrast to the results here. Oginuma et al found that inhibition of glycolysis or beta-catenin acetylation does not affect beta-catenin stability (Nature 584:98), again in contrast to these results. Another paper showed that acidification inhibits Wnt signaling by promoting the expression of a transcriptional repressor and not via beta-catenin stability (Cell Discovery 4:37). There are also additional papers showing increased pH can promote cell proliferation via other mechanisms (e.g. Nat Metab 2:1212). It is possible that there is organ-specificity in these signaling pathways however some clarification of these divergent results is warranted.
The pleiotropic actions of Wnt signaling on cell proliferation and differentiation are well known, even shifting from pro-proliferative to anti-proliferative depending on tissue or cell type. It is thus not surprising that different studies found unique effects of pH and glycolysis on b-catenin modifications and the activation of downstream signaling. Thus, as suggested by the reviewer, the difference between our data and other studies could be attributed to tissue and organism. In our revision, we will more fully assess our findings in the context of published studies, as recommended by the reviewer.
To summarize our data, in the developing retina, we found that non-phosphorylated b-catenin protein levels increase in Pten-cKO retinas in vivo, while conversely, non-phosphorylated b-catenin protein levels decrease upon 2DG treatment and at low pH 6.5 in vitro.
The Oginuma et al. 2020 (Nature 584: 98-101) study was performed on the chick tailbud and investigated lineage decisions by neuromesodermal progenitors in the presomitic mesoderm. In this context, WNT activity, glycolysis and pHi all decline in tandem, complementary to our findings. However, Oginuma et al. found that while phosphorylated and non-phosphorylated b-catenin levels do not vary, K49 b -catenin acetylation is reduced at low pHi. In their system, K49 b -catenin acetylation is associated with a switch in cell fate choice from neural to mesodermal in the chick tailbud. We will now assess this modification.
Hauck et al. 2021 (Cell Death & Differentiation 28:1398-1417) found that by mutating Pkm, a rate-limiting glycolytic enzyme, b-catenin can more efficiently shuttle to the nucleus to activate Wnt-signaling and promote cardiomyocyte proliferation. This study highlights the importance of examining b-catenin protein levels in both cytoplasmic and nuclear fractions. They also examined transcriptional targets of Wnt signaling, such as Axin2, Ccnd1, Myc, Sox2 and Tnnt3, which we will also now assess.
In a separate study in cancer cells, high pH leads to increased expression of Ccnd1, a b-catenin target gene, and promotes proliferation (Koch et al. 2020. Nat Metab. 2:1212-1222). These findings are consistent with our demonstration that b-catenin levels are stabilized at pH 8, and RPC proliferation is enhanced. A separate study by Melnik et al 2018 (Cell Discovery 4:37) performed in cancer cells found that acidification induced by metformin indirectly suppresses Wnt signaling by activating the DDIT3 transcriptional repressor, consistent with our data showing low pH suppresses b-catenin stability. Melnik et al also used Mcl inhibitors, as we did in our study, and showed that this treatment blocked Wnt signaling. While we did not look at the impact of CNCn on Wnt signaling, we did see a decline in proliferation, as expected if Wnt levels are low. The relationship between CNCn and Wnt activity will now be assessed.
The one study that fits less well is from Czowski and White (BioRxiv), where they found that higher pH levels decrease b-catenin levels in the cytoplasm, nucleus and junctional complexes in MDCK cells. In this study, the authors altered pH using inhibitors for a sodium-proton exchanger and a sodium bicarbonate transporter. The Oginuma paper instead used the ionophores nigericin and valinomycin to equilibrate intracellular pHi to media pH, which we will now incorporate into our study.
In summary, to more comprehensively examine the link between Pten loss, glycolytic activity, pHi and Wnt signaling, we will examine levels of phosphorylated, non-phosphorylated and K49 acetylated b-catenin after each manipulation (i.e., Pten loss, pH manipulations, CNCn treatment, glycolysis inhibition, acetate treatments). For pH manipulations, we will use nigericin and valinomycin to equilibrate pH. These studies will be performed on cytoplasmic and nuclear fractions from CD133+ MACS-enriched RPCs, to add cell type and stage specificity to our study. We will also use qPCR to examine Wnt signaling genes, such as Axin2, Ccnd1, Myc, Sox2 and Tnnt3.
(5) The gene expression analysis is not completely convincing. E.g. the expression of additional glycolytic genes should be shown in Figure 1. It is not clear why Hk1 and Pgk1 are specifically shown, and conclusions about changes in glycolysis are difficult to draw from the expression of these two genes. The increase in glycolytic gene expression in the Pten-deficient retina is generally small.
See response to point 3.
(6) Is it possible that glycolytic inhibition with 2DG slows down the development and production of most newly differentiated cells rather than specifically affecting photoreceptor differentiation?
We thank the reviewer for this excellent suggestion. We will examine the impact of 2DG on the differentiation of other retinal cell types, including bipolar and amacrine cells and Muller glia. For technical reasons, we will exclude ganglion cells, which die in culture and are not possible to examine in explants, and horizontal cells, which are a rare cell type, and hence, difficult to accurately quantify.
(7) Are the prematurely-born cells caused by PFKFB3 overexpression photoreceptors as assessed by morphology or markers (in addition to position)?
We will immunostain treated retinas with additional cell-type specific markers to examine rod and cone photoreceptor numbers and morphologies.
Reviewer #2 (Public review):
Summary:
The manuscript by Hanna et al., addresses the question of energy metabolism in the retina, a neuronal tissue with an inordinately high energy demand. Paradoxically, the retina appears to employ to a large extent glycolysis to satisfy its energetic needs, even though glycolysis is far less efficient than oxidative phosphorylation (OXPHOS). The focus of the present study is on the early development of the retina and the retinal progenitor cells (RPCs) that proliferate and differentiate to form the seven main classes of retinal neurons. The authors use different genetic and pharmacological manipulations to drive the metabolism of RPCs or the retina towards higher or lower glycolytic activity. The results obtained suggest that increased glycolytic activity in early retinal development produces a more rapid differentiation of RPCs, resulting in a more rapid maturation of photoreceptors and photoreceptor segment growth. The study is significant in that it shows how metabolic activity can determine cell fate decisions in retinal neurons.
Strengths:
This study provides important findings that are highly relevant to the understanding of how early metabolism governs the development of the retina. The outcomes of this study could be relevant also for human diseases that affect early retinal development, including retinopathy of maturity where an increased oxygenation likely causes a disturbance of energy metabolism.
We thank the reviewer for these positive comments on our study.
Weaknesses:
The restriction to only relatively early developmental time points makes it difficult to assess the consequences of the different manipulations on the (more) mature retina. Notably, it is conceivable that early developmental manipulations, while producing relevant effects in the young post-natal retina, may "even out" and may no longer be visible in the mature, adult retina.
While we agree that it would be interesting to observe the long-term consequences of our manipulations, we are limited by our retinal explant model, which can at best be cultured for 2 weeks in vitro. Additional limitations include the lack of photoreceptor outer segment development in our in vitro model. However, we can perform more extensive analyses of our genetic models in vivo (i.e., Pten-cKO, cyto-PFKB3-GOF, Ctnnb1-cKO). For these lines, we will focus on more in-depth analyses of photoreceptor differentiation and outer segment maturation using additional markers and one later stage of development.
Reviewer #3 (Public review):
Summary:
This study examines the metabolic regulation of progenitor proliferation and differentiation in the developing retina. The authors observe dynamic changes in glycolytic gene expression in retinal progenitors and use various strategies to test the role of glycolysis. They find that elevated glycolysis in Pten-cKO retinas results in alteration of RPC fate, while inhibition of glycolysis has converse effects. They specifically test the role of elevated glycolysis using dominant active cytoPFKB3, which demonstrates the selective effects of elevated glycolysis on progenitor proliferation and rod differentiation. They then show that elevated glycolysis modulates both pHi and Wnt signaling, and provide evidence that these pathways impact proliferation and differentiation of progenitors, particularly affecting rod photoreceptor differentiation.
Strengths:
This is a compelling and rigorous study that provides an important advance in our understanding of metabolic regulation of retina development, addressing a major gap in knowledge. A key strength is that the study utilizes multiple genetic and pharmacological approaches to address how both increased or decreased glycolytic flux affect retinal progenitor proliferation and differentiation. They discover elevated Wnt signaling pathway genes in Pten cKO retina, revealing a potential link between glycolysis and Wnt pathway activation. Altogether the study is comprehensive and adds to the growing body of evidence that regulation of glycolysis plays a key role in tissue development.
We thank the reviewer for these positive comments on our study.
Weaknesses:
(1) Following the expression of cytoPFKB3, which results in increased glycolytic flux, BrDU labeling was performed at e12.5 and increased labeled cells were detected in the outer nuclear layer. However whether these are cones or rods is not established. The rest of the analysis is focused on the precocious maturation of rhodopsin-labeled outer segments, and the major conclusions emphasize rod photoreceptor differentiation. Therefore, it is unclear whether there is an effect on cone differentiation for either Pten cKO or cytoPFKB3 transgenic retina. It is also not established whether rods are born precociously. Presumably, this would be best detected by BrDU labeling at later embryonic stages.
We agree with the reviewer that we should expand our study to also examine cone differentiation and outer segment maturation, which we will now do by adding additional markers to our study.
(2) The authors find that there is upregulation of multiple Wnt pathway components in Pten cKO retina. They further show that inhibiting Wnt signaling phenocopies the effects of reducing glycolysis. However, they do not test whether pharmacological inhibition of Wnt signaling reverses the effects of high glycolytic activity in Pten cKO retinas. Thus the argument that Wnt is a key downstream effector pathway regulating rod photoreceptor differentiation is weak.
See Reviewer 1, point 1
(3) The use of sodium acetate to force protein acetylation is quite non-specific and will have effects beyond beta-catenin acetylation (which the authors acknowledge). Thus it is a stretch to state that "forced activation of beta-catenin acetylation" mimics the impact of Pten loss/high glycolytic activity in RPCs since the effects could be due to acetylation of other proteins.
As outlined in our response to Reviewer #1, point 4, we will now assess K49 b-catenin acetylation levels, as conducted by Oginuma et al. This analysis will allow us to determine whether b-catenin acetylation is altered with manipulations of Pten, glycolysis, pH or acetate treatments.
