kotahi

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eLife Assessment

This valuable study proposes a novel rapid-entry mechanism for S. aureus, involving the rapid release of calcium from lysosomes. The paper's strength lies in its very interesting hypothesis. The methods used are solid and adequately support the conclusions.

Reviewer #2 (Public review):

In the manuscript Ruhling et al propose a rapid uptake pathway that is dependent on lysosomal exocytosis, lysosomal Ca2+ and acid sphingomyelinase, and further suggest that the intracellular trafficking and fate of the pathogen is dictated by the mode of entry. Overall, this is manuscript argues for an important mechanism of a 'rapid' cellular entry pathway of S.aureus that is dependent on lysosomal exocytosis and acid sphingomyelinase and links the intracellular fate of bacterium including phagosomal dynamics, cytosolic replication and host cell death to different modes of uptake.

Key strength is the nature of the idea proposed, while continued reliance on inhibitor treatment combined with lack of phenotype / conditional phenotype for genetic knock out is a major weakness.

In the revised version, the authors perform experiments with ASM KO cells to provide genetic evidence of the role for ASM in S. aureus entry through lysosomal modulation. The key additional experiment is the phenotype of reduced bacterial uptake in low serum, but not in high serum conditions. The authors suggest this could be due to the SM from serum itself affecting the entry. While this explanation is plausible, prolonged exposure of cells to low serum is well documented to alter several cellular functions, particularly in the context of this manuscript, lysosomal positioning, exocytosis and Ca2+ signaling. A better control here could be WT cells grown in low serum. If SM in serum can interfere, why do they see such pronounced phenotype on bacterial entry in WT cells upon chemical inhibition?

While the authors argue a role for undetectable nano-scale Cer platforms on the cell surface caused by ASM activity, results do not rule out a SM independent role in the cellular uptake phenotype of ASM inhibitors.

The authors have attempted to address many of the points raised in the previous revision. While the new data presented provide partial evidence, the reliance on chemical inhibitors and lack of clear results directly documenting release of lysosomal Ca2+, or single bacterial tracking, or clear distinction between ASM dependent and independent processes dampen the enthusiasm.

I acknowledge the author's argument of different ASM inhibitors showing similar phenotypes across different assays as pointing to a role for ASM, but the lack of phenotype in ASM KO cells is concerning. The author's argument that altered lipid composition in ASM KO cells could be overcoming the ASM-mediated infection effects by other ASM-independent mechanisms is speculative, as they acknowledge, and moderates the importance of ASM-dependent pathway. The SM accumulation in ASM KO cells does not distinguish between localized alterations within the cells. If this pathway can be compensated, how central is it likely to be ?

The authors allude to lower phagosomal escape rate in ASM KO cells compared to inhibitor treatment, which appears to contradict the notion of uptake and intracellular trafficking phenotype being tightly linked. As they point out, these results might be hard to interpret. Could an inducible KD system recapitulate (some of) the phenotype of inhibitor treatment? If S. aureus does not escape phagosome in macrophages, could it provide a system to potentially decouple the uptake and intracellular trafficking effects by ASM (or its inhibitor treatment) ?

The role of ASM on cell surface remains unclear. The hypothesis proposed by the authors that the localized generation of Cer on the surface by released ASM leads to generation of Cer-enriched platforms could be plausible, but is not backed by data, technical challenges to visualize these platforms notwithstanding. These results do not rule out possible SM independent effects of ASM on the cell surface, if indeed the role of ASM is confirmed by controlled genetic depletion studies.

The reviewer acknowledges technical challenges in directly visualizing lysosomal Ca2+ using the methods outlined. Genetically encoded lysosomal Ca2+ sensor such as Gcamp3-ML1 might provide better ways to directly visualize this during inhibitor treatment, or S. aureus infection.

Author response:

The following is the authors’ response to the previous reviews

Public Reviews:
Reviewer #2 (Public review):
In the manuscript, Ruhling et al propose a rapid uptake pathway that is dependent on lysosomal exocytosis, lysosomal Ca2+ and acid sphingomyelinase, and further suggest that the intracellular trafficking and fate of the pathogen is dictated by the mode of entry. Overall, this is manuscript argues for an important mechanism of a 'rapid' cellular entry pathway of S.aureus that is dependent on lysosomal exocytosis and acid sphingomyelinase and links the intracellular fate of bacterium including phagosomal dynamics, cytosolic replication and host cell death to different modes of uptake.
Key strength is the nature of the idea proposed, while continued reliance on inhibitor treatment combined with lack of phenotype for genetic knock out is a major weakness.

We agree with the reviewer that a S. aureus invasion phenotype in ASM K.O. cells would unequivocally demonstrate the importance of ASM for the process. In the revised manuscript, we report an invasion phenotype in ASM K.O. cells. The absence of an invasion phenotype in ASM K.O. cells in our original experiments was likely caused by SM accumulation in ASM-depleted cells originating from FBS (see Figure 2I, in the revised manuscript).

We thus cultured cells for up to three days in 2% FBS and then reduced the concentration to 1% FBS one day prior to experimentation. Under these conditions reduced S. aureus invasion in ASM K.O.s was observed when compared to wildtype cells.

This was not detected when we cultured the cells in medium containing the common concentration of 10% FBS. Our new data supports the results we acquired with three different ASM inhibitors.

The invasion defect in ASM K.O.s cultured in low FBS was more pronounced at 10 min p.i. when compared to the 30 minute time point (Figure 2K), further corroborating that the ASM-dependent invasion pathway is relevant early in infection. This is consistent with the invasion dynamics we observed upon interference with lysosomal Ca2+ signaling [TPC1 K.O. (Figure 1C), BAPTA-AM (Figure 3D)], lysosomal exocytosis [Syt7 K.O. (Figure 2F), Ionomycin (Figure 3D)] and ASM activity by inhibitor treatment (Figure 3D).

Originally, we had hypothesized that changes in the sphingolipidome induced by absence of ASM may have caused the lack of an S. aureus invasion phenotype. We thus compared the sphingolipidome of ASM K.O.s cultured in 1% and 10% FBS. Indeed, SM accumulation was less severe when we cultured the cells in 1% FBS (Figure 2M and Supp. Figure 3). Hence, we think that strong SM accumulations in ASM K.O. cells cultured in 10% FBS may facilitate ASM-independent invasion mechanisms and thus, the absence of ASM-dependent invasion could not be detected by analyzing the number of invaded bacteria. This is supported by experiments, where we treated ASM K.O.s with the ASM inhibitor ARC39, which only slightly affected S. aureus invasion, whereas we detected a strong reduction of internalized bacteria by ARC39 treatment of WT cells (Figure 2 J). We think that this experiment and the reduced invasion in ASM K.O.s rule out an ASM/SM-independent effect of the inhibitors.

- While the authors argue a role for undetectable nano-scale Cer platforms on the cell surface caused by ASM activity, results do not rule out a SM independent role in the cellular uptake phenotype of ASM inhibitors.

We agree with reviewer that we do not show formation of ceramide-enriched platforms, and we thus changed the manuscript accordingly (see below).

- The authors have attempted to address many of the points raised in the previous revision. While the new data presented provide partial evidence, the reliance on chemical inhibitors and lack of clear results directly documenting release of lysosomal Ca2+, or single bacterial tracking, or clear distinction between ASM dependent and independent processes dampen the enthusiasm.

We shared the reviewer’s desire to discriminate between ASM-dependent and ASM-independent processes, but we are limited by cell biology and the simultaneous occurrence of processes - here the uptake of bacteria by multiple pathways.

However, we were able to address ASM-dependency of our rapid uptake mechanism by observing a genetic phenotype in SMPD1 knockout-cells.

We here do not make any assumptions on the centrality of the pathway and its importance in vivo. As scientists we were interested in the fact that such an ASM dependent pathway existed. In different as of yet still unidentified cell lines such a pathway may pose the main entry point for bacteria. Or maybe it represent an ASM-dependent mode of receptor uptake which we have identified with the bacteria piggy-backing into the cells.

- I acknowledge the author's argument of different ASM inhibitors showing similar phenotypes across different assays as pointing to a role for ASM, but the lack of phenotype in ASM KO cells is concerning. The author's argument that altered lipid composition in ASM KO cells could be overcoming the ASM-mediated infection effects by other ASM-independent mechanisms is speculative, as they acknowledge, and moderates the importance of ASM-dependent pathway. The SM accumulation in ASM KO cells does not distinguish between localized alterations within the cells. If this pathway can be compensated, how central is it likely to be?

We are convinced that our new genetic evidence of an S. aureus invasion phenotype in ASM K.O.s will eliminate the reviewer’s concerns about the role of ASM during the bacterial invasion.

The new lipidomics data of ASM K.O.s cultured in 1% and 10% FBS (Figure 2, M, Supp. Figure 3) and inhibitor-treated WT cells (Figure 2L, Supp. Figure 3) show a correlation between SM accumulation and the invasion phenotype.

We agree with the reviewer, however, that the reason why changes in sphingolipidome increase ASM-independent S. aureus internalization by host cells remains elusive. One possible explanation is a dysfunction of the lipid raft-associated protein caveolin-1 upon strong SM accumulation, which was previously shown to appear in ASM-deficient cells (1, 2). A lack of caveolin-1 results in strongly increased host cell entry of S. aureus (3, 4). Characterization of the mechanism behind these observations requires further experimentation and is beyond the scope of the current manuscript.

Host cells possess mechanisms to prevent infections, while pathogens developed strategies to circumvent these defense processes. In the present scenario, a physiological membrane composition of the host cell represents such a pathogen defense mechanism (as shown e.g. for caveolin-1 that restricts invasion of S. aureus in healthy cells). If a defense mechanism is disabled (as we speculate it is the case upon strong SM accumulation in ASM K.O.s cultured in 10%FBS), infection is facilitated. In healthy WT cells, these mechanisms (e.g. caveolin-1) are functional and, hence, we would not expect a “compensation” of ASM-dependent invasion. We here analyze invasion events that cannot be prevented by host defense mechanisms as they occur in untreated WT cells and are absent upon interfering with the ASM-dependent invasion pathway (by inhibitors and genetic K.O.). Thus, we think the ASM-dependent pathway, which mediates 50-70% of bacteria internalized by healthy WT cells 10 min p.i., is central for the infection.

- The authors allude to lower phagosomal escape rate in ASM KO cells compared to inhibitor treatment, which appears to contradict the notion of uptake and intracellular trafficking phenotype being tightly linked. As they point out, these results might be hard to interpret.

We measured phagosomal escape of S. aureus JE2 in ASM K.O. cells cultured in 1% FBS. Again, we infected cells for 10 or 30 min and determined the escape rates 3h p.i. However, the results are similar to escape rates determined with 10% FBS (Author response image 1).

Escape rates of S. aureus were significantly decreased in absence of ASM regardless of the FBS concentration in the medium. We therefore think that prolonged absence of ASM has other side effects. For instance, certain endocytic pathways could be up- or down-regulated to adapt for the absence of ASM or could be affected by other changes in the lipidome (that can be minimized but not completely prevented by culturing cells in 1% FBS). This could, for instance, affect maturation of S. aureus-containing phagosomes and hence phagosomal escape.

Author response image 1.

As it is unclear how prolonged absence of ASM can affect cellular processes, we think other experiments investigating the role of ASM-dependent invasion for phagosomal escape are more reliable. Most importantly, bacteria that enter host cell early during infection (and thus, predominantly via the “rapid” ASM-dependent pathway) possess lower phagosomal escape rates than bacteria that entered host cells later during infection (Figure 5, D and E). This is confirmed by higher escapes rates upon blocking ASM-dependent invasion with Vacuolin-1 (Figure 4E) and three different ASM inhibitors (Figure 4C and D). We further demonstrate that sphingomyelin on the plasma membrane during invasion influences phagosomal escape, while sphingomyelin levels in the phagosomal membrane did not change phagosomal escape (Figure5 a and b). This is summarized in Figure 5F.

- Could an inducible KD system recapitulate (some of) the phenotype of inhibitor treatment ? If S. aureus does not escape phagosome in macrophages, could it provide a system to potentially decouple the uptake and intracellular trafficking effects by ASM (or its inhibitor treatment)?

Inducible knock-downs in our laboratory are based on the vector pLVTHM in cells co-expressing the repressor TetR fused to a KRAB domain. It needs to be stated that for optimal knock-downs the induction has to be performed by doxycycline supplementation in the medium for 7 days thus leading to several days of growth of the cells, which will allow the cells to adapt their lipid metabolism thus reflecting a situation that we encounter for the K.O.s.

ASM-dependent uptake of S. aureus in macrophages has been demonstrated before (5). However, the course of infection in macrophages differs from non-professional phagocytes (6). E.g. in macrophages, S. aureus replicates within phagosomes, whereas in non-professional phagocytes replicates in the host cytosol. Absence of ASM therefore may influence the intracellular infection of macrophages with S. aureus in a distinct manner.

- The role of ASM on cell surface remains unclear. The hypothesis proposed by the authors that the localized generation of Cer on the surface by released ASM leads to generation of Cer-enriched platforms could be plausible, but is not backed by data, technical challenges to visualize these platforms notwithstanding. These results do not rule out possible SM independent effects of ASM on the cell surface, if indeed the role of ASM is confirmed by controlled genetic depletion studies.

We agree with the reviewer that we do not show generation of ceramide-enriched platforms. We thus changed Figure 6F in the revised manuscript to make clear that it remains elusive whether ceramide-enriched platforms are formed. We also added a sentence to the discussion (line 615) to emphasize that the existence of these microdomains is still debated in lipid research.

We think that the following observations support SM-dependent effects of ASM during S. aureus invasion:

(i) reduced invasion upon removing SM from the plasma membrane (Figure 2N, Supp. Figure 2M)

(ii) increased invasion in TPC1 and Syt7 K.O. (Figure 2, P) in presence of exogenously added SMase.

However, we agree with the reviewer that we do not directly demonstrate ASM-mediated SM cleavage during S. aureus invasion. Hence, we added a sentence to the discussion that mentions a possible SM-independent role of ASM for invasion (line 556) that reads:

“Since it remains elusive to which extent ASM processes SM on the plasma membrane during S. aureus invasion, one may speculate that ASM could also have functions other than SM metabolization during host cell entry of the pathogen. However, we did not detect a direct interaction between S. aureus and ASM in an S. aureus-host interactome screen (7).”

- The reviewer acknowledges technical challenges in directly visualizing lysosomal Ca2+ using the methods outlined. Genetically encoded lysosomal Ca2+ sensor such as Gcamp3-ML1 might provide better ways to directly visualize this during inhibitor treatment, or S. aureus infection.

We thank the reviewer for this suggestion. We included the following section in our discussion (line 593):

“Since fluorescent calcium reporters allow to monitor this process microscopically (8, 9) ,future experiments may visualize this process in more detail and contribute to our understanding of the underlying signaling. mechanisms.”

References

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(2) J. Rappaport, R. L. Manthe, C. Garnacho, S. Muro, Altered Clathrin-Independent Endocytosis in Type A Niemann-Pick Disease Cells and Rescue by ICAM-1-Targeted Enzyme Delivery. Mol Pharm 12, 1366-1376 (2015).

(3) C. Hoffmann et al., Caveolin limits membrane microdomain mobility and integrin-mediated uptake of fibronectin-binding pathogens. J Cell Sci 123, 4280-4291 (2010).

(4) L.-P. Tricou et al., Staphylococcus aureus can use an alternative pathway to be internalized by osteoblasts in absence of β1 integrins. Scientific Reports 14, 28643 (2024).

(5) C. Li et al., Regulation of Staphylococcus aureus Infection of Macrophages by CD44, Reactive Oxygen Species, and Acid Sphingomyelinase. Antioxid Redox Signal 28, 916-934 (2018).

(6) A. Moldovan, M. J. Fraunholz, In or out: Phagosomal escape of Staphylococcus aureus. Cell Microbiol 21, e12997 (2019).

(7) M. Rühling, F. Schmelz, A. Kempf, K. Paprotka, J. Fraunholz Martin, Identification of the Staphylococcus aureus endothelial cell surface interactome by proximity labeling. mBio 0, e03654-03624 (2025).

(8) D. Shen et al., Lipid storage disorders block lysosomal trafficking by inhibiting a TRP channel and lysosomal calcium release. Nat Commun 3, 731 (2012).

(9) L. C. Davis, A. J. Morgan, A. Galione, NAADP-regulated two-pore channels drive phagocytosis through endo-lysosomal Ca(2+) nanodomains, calcineurin and dynamin. EMBO J 39, e104058 (2020).