The inhibition of LSD1 via sequestration contributes to tau-mediated neurodegeneration

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Abstract

We have made the discovery that pathological tau functions through the histone demethylase LSD1 in the Alzheimer’s disease pathway. Thus, we have identified a mechanism that links tau to the downstream neuronal dysfunction pathways. This step can potentially be targeted therapeutically, after the onset of dementia symptoms, to block the progression of dementia in Alzheimer’s disease patients.

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    Reply to the reviewers

    We thank the reviewers for their close reading and constructive comments on our manuscript. We believe that their insight has substantially strengthened our manuscript. Please find our response/revision plan for each comment below (in bold).

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

    This is a very interesting study that addresses an important topic. In brief, the authors build on their previous data showing that LSD1 seems to be neuroprotective. Here they follow the hypothesis that Tau-dependent sequestration of LSD1 to the cytoplasm leads to loss of nuclear LSD1 function. Crossing Tau mutant mice (PS19) to heterozyous LSD1 knock out mice exacerbates phenotypes in PS19 mice, while viral overexpression of LSD1 rescues part of these phenotypes.

    As said the data is interesting but lack mechanistic explanation that would allow in my view publication in a very high profile journal. Moreover, there are some data such as the RNA-seq that would not be acceptable in the present for by any journal. However, all of these issues could be addressed by the authors in case reviewers would refer to them.

    The sequestration of LSD1 in the cytoplasm by tau, along with the co-localization of LSD1 with tau in human cases (in our previous Nature Communications paper-Christopher et al. 2017) provide a mechanistic explanation (sequestration) for why we are able to exacerbate and rescue tau-mediated neurodegeneration by modulating LSD1. As the reviewer pointed out, we believe that we can address all of the critiques brought up (see responses below). By addressing these critiques we believe that we can further substantiate the mechanism underlying our ability to functionally modulate tau-mediated neurodegeneration in vivo.

    **Here are some specific issues.**

    1 . Especially the proposed link of Tau-mediated sequestration of LSD1 to the cytoplasm is not fully supported by the data. A key finding shows that LSD1 is seen more in cytoplasm in PS19 mice. However, the biological relevance of this observation cannot be fully appreciated at present, since the magnitude of this phenotype is unclear. Approaches to perform a quantitative analysis in addition to the representative IHC images would be helpful.

    __The change in localization of LSD1 from nuclear to cytoplasmic that we observe in Tau PS19 mice is dramatic. We tried to convey this magnitude of sequestration in different brain regions by showing a range of representative images. Consistent with this, Reviewer 2 commented that “__These data are very strong, the effect is impressive.” __Nevertheless, we can attempt to further quantify the change in localization. To accomplish this, we can try two different methods. (1) We can add a nuclear marker and attempt to quantify the level of nuclear versus cytoplasmic LSD1 from the immunofluorescence images. (2) We can also attempt to generate nuclear versus cytoplasmic fractions and quantify LSD1 levels by western blot. __

    2 . Point 1 might be of specific importance since the subsequent experiments built on the idea that mice with already recued LSD1 levels should have a more severe phenotype in case of Tau pathology. However, they do not really address the role of Tau-mediated sequestration of LSD1 anymore. The authors employ mice that constitutively lack one allele of LSD1 which generally leads to a more severe phenotype in PS19 mice. This is very interesting, but I wonder if reduced LSD1 levels might generally put the network in a more vulnerable state and that other detrimental stimuli that do not cause intracellular protein aggregation might have a similar effect. The authors realize this and address this question by comparing via RNA-seq the gene-expression changes observed in Lsd1+/+, Lsd1Δ/+, PS19 Tau, and PS19;Lsd1Δ/+ littermates. Comparatively few changes are observed. However, the major issue with this experiment is that an n=2/group is simply no acceptable anymore to be published in any serious journal. Thus, this data is not interpretable as it stands.

    __To further address the role of tau-mediated sequestration of LSD1, we can attempt to quantify (see above) nuclear versus cytoplasmic LSD1 in PS19 Tau mice with heterozygous *Lsd1, *and compare it to the level of sequestration observed in PS19 Tau mice alone. __

    __To strengthen the RNAseq data, we can perform two additional replicates.____However, because (1) the RNAseq results were only used for genome-wide comparisons, (2) the replicates were very tight, and (3) the results were clear, it is very unlikely that additional replicates are going to alter the result. Thus, alternatively we might be able to alter the language of the manuscript to qualify the result somewhat. In this regard, it should be noted that reviewer 2 commented that “__The data are very convincing, and provide a strong molecular base showing a tight overlap in the effected molecular pathways associated with both pathological tau and Lsd1 heterozygosity.” __Reviewer 3 also commented that the transcriptomic dataset “__strengthen some of the conclusions.”

    Reviewer #1 (Significance (Required)):

    The data will be interesting to the field and help to further understand the role of LSD1 in neuroegenerative dieases linked to tauopathy.

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

    The manuscript "The inhibition of LSD1 via sequestration contributes to tau-mediated neurodegeneration" by Amanda K. Engstrom, Alicia C. Walker, Rohitha A. Moudgal, Dexter A. Myrick, Stephanie M. Kyle and David J. Katz, is an excellent study that beautifully describes the implication of the epigenetic enzyme LSD1, as downstream mediator of tau pathology in neurodegenerative disease.

    The same authors in a previous paper showed that i) loss of LSD1 in the adult mouse brain, leads to significant neuronal cell death and ii) loss of LSD1 induces genome-wide expression changes that significantly overlap with those observed in the brains of postmortem human AD. In this work, are presented initial evidences that in AD brain, LSD1 nuclear function could be disrupted by mislocalization to pathological tau.

    In the present work, using the PS19 mouse model, the authors provide the first cytological evidence that pathological tau can prevent LSD1 from properly localizing to the nucleus in hippocampal and cortical neurons. These data are very strong, the effect is impressive. Crossing the PS19 mouse model of taupathology with a mouse model of LSD1 brain heterozygosity LSD1Δ /+, the authors provide functional data that the inhibition of LSD1 function contributes to tau induced neurodegeneration. Indeed, several pathological parameters measured in the PS19 mouse model, are exacerbated in a reduced genetic LSD1 background. Survival rate, motor activity measured with a rotarod test. The behavioral analysis is nicely paralleled by the analysis of spinal cord motor neurons, showing abnormal morphology in the double mutant mice, compared to the PS19. Overall morphology of the hippocampus shows decreased brain size and brain weight. The analysis is accompanied by MRI analysis, showing again very impressive results, with the double mutant being the most affected and the LSD1Δ /+ very similar to WT.

    The second part of the work is aimed at demonstrating specificity of the functional interaction between tau pathology and LSD1. The authors provide a very well planned transcriptional profiling of the different mouse models, choosing the most relevant time point (prior the onset of neuronal cell death), very clearly justifying the rational of their choice. The data are very convincing, and provide a strong molecular base showing a tight overlap in the effected molecular pathways associated with both pathological tau and Lsd1 heterozygosity. As final approach, the authors rescue neurodegeneration in the hippocampus of PS19 Tau mice overexpressing LSD1 using a neuron-specific virus. Overall, these data establish LSD1 as a major downstream effector of tau-mediated neurodegeneration indicating that the LSD1 pathway is a potential late stage target for intervention in tauopathies, such as AD.

    **Minor point:**

    In material and Methods is missing a section dedicated to a detailed description of statistical analysis.

    We have added a section to the materials and methods dedicated to a detailed description of statistical analysis (lines 509-518).

    Reviewer #2 (Significance (Required)):

    I believe that this work will be of great interest for the neurodegenerative together with the neuro-epigenetic field (my personal area of expertise). The identification of a clear new pathway implicated in AD and neurodegeneration together with the suggestion of a possible new therapeutic target (disruption of tau-LSD1 interaction) is of high potential impact for future studies.

    We really appreciate this very positive review, which acknowledges the thoroughness of our results, the mechanistic insight that we provided and the “high potential impact” of our work.

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

    The work on LSD1 in this manuscript is based on earlier studies that deleting the histone demethylase Lsd1 in adult mice leads to neuronal cell death and that the neurofibrillary tangles in Alzheimer's disease brains can be stained for LSD1.

    The manuscript first shows that LSD1 is sequestered in PS19 tau transgenic mice, that a reduction of Lsd1 exacerbates the pathology and that overexpression rescues, complemented by a separate transcriptomic dataset used to strengthen some of the conclusions. As it currently stands, in my view, this work is very preliminary, and I am not sharing all conclusions made by the authors.

    **My specific points are following the headers of the Results section:**

    (1) Tau pathology depletes LSD1 from the nucleus in the PS19 Tau mouse model: What is clear from the images is that in the PS19 Tau tg mice LSD1 is depleted from the nucleus. What is not correct is that in WT it is only localized to the nucleus. What should be done, is to quantify the relative localization to the two compartments. In addition, a subcellular fractionation could be performed (see point further below).

    LSD1 is strictly a nuclear protein with a well-defined nuclear localization signal that interacts with the importin ____a____complex (Jin et al, J. Biochem 2014). Reference to this has been added to the text in the introduction (lines 53-54) and in the results (line 87-89). Nevertheless, we can also attempt subcellular fractionation and localization of LSD1 in the nuclear versus cytoplasmic fraction (see response to reviewer 1 above).

    (2) Reduction of LSD1 increases the mouse tauopathy phenotype: 2.1. The PS19 Tau Tg mice have been crossed with an Lsd1 heterozygous mutant (LSD1 delta/-). I tried to find the reference as to how this mutant has actually been made (refs 32-34). Ref 32 describes a conditional KO (The position of the gene trap insertion (STOP), downstream of exon 3, truncates the LSD1 open reading frame within the SWIRM domain prior to the amine oxidase domain, which is essential for the catalytic activity of LSD1), which leaves a 210 amino acid truncated protein which is an obvious confound which should be mentioned and discussed. Besides from that, it is not clear to me how the Lsd1 gene was deleted for the current study, i.e. which promoter has been used.

    The *Lsd1 allele used in this study was generated in the Rosenfeld lab (Wang et al., Nature 2007). This was stated in the acknowledgements, but has now been added to both the main text (lines 105-109) and the methods (lines 386-391) for clarity. ThisLsd1 *allele is a null allele that has also been used previously by both our group, as well as by additional groups (For example: Christopher et al., Nature Communications 2017 and Lyons et al., Cell 2013). In this current study, *Lsd1 was deleted with the Vasa-Cre *transgenic line. Once the deletion allele passes through the germline, *Lsd1 *is heterozygous throughout the mouse. We deeply regret this oversight.

    2.2. Fig S2 shows that LSD1 is reduced in the heterozygote, but increased in PS19 by 20% and then again decreased in the PS19 x LSD1 delta/-. Clearly, a subcellular fractionation or histological quantification is needed to understand what the levels are in the cytoplasm as compared to the nucleus.

    The data referred to in Figure S2 is from bulk brain homogenate showing that there is a reduction of LSD1 in mice carry the deletion allele both in a wild-type and PS19 Tau background. Nevertheless, we can attempt subcellular fractionation and quantification of LSD1 localization in the nucleus versus cytoplasm (see response to reviewer 1 above) to further clarify this result.

    2.3. The rescue in Fig 2A is really modest. Certainly, with tau in PS19 potentially trapping LSD1 in the cytoplasm there should be less of LSD1 in the nucleus when there is only one functioning allele. What is needed is a quantification of nuclear and cytoplasmic LSD1 in the genotypes.

    We can attempt subcellular fractionation and quantification of LSD1 localization in the nucleus versus cytoplasm (see response to reviewer 1 above) to further clarify this result.

    2.4. I don't agree with the statement: 'started only slightly earlier than PS19 Tau mice, but after the appearance of pathological tau in neurons (p. 6)' as tau pathology develops gradually and is present before the age of 6 months in this strain.

    This statement refers specifically to the AT8 positive pathology that was quantified in this manuscript (Figure S6). This quantification shows that AT8 positive pathology is present in the hippocampus and cortex, when PS19 Tau mice with reduced LSD1 begin to decline. The text has been amended to clarify this (line 124-125).

    (3) Tau pathology is not affected by change in LSD1 levels: This is to be expected as Tau is upstream of LSD1 in a pathocascade.

    __The quantification of tau pathology was included as a negative control. As we expected, tau pathology is not affected by the change in LSD1 levels. As the reviewer correctly points out, this data is consistent with our model, that tau pathology is upstream of LSD1. __

    (4) The functional interaction between tau pathology and LSD1 inhibition is specific: The specificity of the interaction needs to be tested by co-immunoprecipitations or proximity ligation assays and by mapping which domains of LSD1 and Tau have a role in trapping, using the appropriate positive and negative controls, as is being routinely done for these kinds of studies.

    We too are very interested in whether LSD1 interacts directly or indirectly with tau pathology, and what domains of LSD1 are required for LSD1 to co-localize with tau pathology. However, to address these questions, we will need to perform multiple biochemical experiments (such as the ones suggested by the reviewer) on mice of different ages, as well as human cases. We believe that this is significantly beyond the scope of the current study, which is focused on the functional interaction between tau pathology and LSD1 in mice.

    (5) Overexpression of LSD1 rescues neurodegeneration in the hippocampus of PS19 Tau mice: The data in Figure 5 are not convincing.

    __It is not clear why the reviewer is not convinced by the rescue data in Figure 5. Reviewer 1 acknowledged that “__viral overexpression of LSD1 rescues part of these phenotypes” __and reviewer 2 agreed that __“the authors rescue neurodegeneration in the hippocampus of PS19 Tau mice overexpressing LSD1 using a neuron-specific virus.”

    **Minor points:**

    Abstract: The statement 'However, the mechanism through which tau contributes to neurodegeneration remains unknown.' is not correct and should be removed. There is a wealth of information on tau-based pathomechanisms available and several studies have identified proteins which become, as seems to be the case for LSD1, trapped by tau in the cytosol.

    This statement in the abstract has been modified (lines 13-15).

    Reviewer #3 (Significance (Required)):

    This form asks me about my expertise. I am working on tau pathomechanisms since more than two decades and the revision experiments I am asking for is what we are doing in our own studies. I find the data on LSD1 interesting, but definitely more work needs to be done to substantiate the claims.

    __We thank the reviewer for their careful reading of the manuscript and appreciate that they found that the data on LSD1 are interesting. __

    Overall, we feel that the reviews of our manuscript are very positive. We hope that our response/revision plan will be suitable for publication.

  2. Note: This preprint has been reviewed by subject experts for Review Commons. Content has not been altered except for formatting.

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    Referee #3

    Evidence, reproducibility and clarity

    The work on LSD1 in this manuscript is based on earlier studies that deleting the histone demethylase Lsd1 in adult mice leads to neuronal cell death and that the neurofibrillary tangles in Alzheimer's disease brains can be stained for LSD1.

    The manuscript first shows that LSD1 is sequestered in PS19 tau transgenic mice, that a reduction of Lsd1 exacerbates the pathology and that overexpression rescues, complemented by a separate transcriptomic dataset used to strengthen some of the conclusions. As it currently stands, in my view, this work is very preliminary, and I am not sharing all conclusions made by the authors.

    My specific points are following the headers of the Results section:

    (1) Tau pathology depletes LSD1 from the nucleus in the PS19 Tau mouse model: What is clear from the images is that in the PS19 Tau tg mice LSD1 is depleted from the nucleus. What is not correct is that in WT it is only localized to the nucleus. What should be done, is to quantify the relative localization to the two compartments. In addition, a subcellular fractionation could be performed (see point further below).

    (2) Reduction of LSD1 increases the mouse tauopathy phenotype: 2.1. The PS19 Tau Tg mice have been crossed with an Lsd1 heterozygous mutant (LSD1 delta/-). I tried to find the reference as to how this mutant has actually been made (refs 32-34). Ref 32 describes a conditional KO (The position of the gene trap insertion (STOP), downstream of exon 3, truncates the LSD1 open reading frame within the SWIRM domain prior to the amine oxidase domain, which is essential for the catalytic activity of LSD1), which leaves a 210 amino acid truncated protein which is an obvious confound which should be mentioned and discussed. Besides from that, it is not clear to me how the Lsd1 gene was deleted for the current study, i.e. which promoter has been used.

    2.2. Fig S2 shows that LSD1 is reduced in the heterozygote, but increased in PS19 by 20% and then again decreased in the PS19 x LSD1 delta/-. Clearly, a subcellular fractionation or histological quantification is needed to understand what the levels are in the cytoplasm as compared to the nucleus.

    2.3. The rescue in Fig 2A is really modest. Certainly, with tau in PS19 potentially trapping LSD1 in the cytoplasm there should be less of LSD1 in the nucleus when there is only one functioning allele. What is needed is a quantification of nuclear and cytoplasmic LSD1 in the genotypes.

    2.4. I don't agree with the statement: 'started only slightly earlier than PS19 Tau mice, but after the appearance of pathological tau in neurons (p. 6)' as tau pathology develops gradually and is present before the age of 6 months in this strain.

    (3) Tau pathology is not affected by change in LSD1 levels: This is to be expected as Tau is upstream of LSD1 in a pathocascade.

    (4) The functional interaction between tau pathology and LSD1 inhibition is specific: The specificity of the interaction needs to be tested by co-immunoprecipitations or proximity ligation assays and by mapping which domains of LSD1 and Tau have a role in trapping, using the appropriate positive and negative controls, as is being routinely done for these kinds of studies.

    (5) Overexpression of LSD1 rescues neurodegeneration in the hippocampus of PS19 Tau mice: The data in Figure 5 are not convincing.

    Minor points:

    Abstract: The statement 'However, the mechanism through which tau contributes to neurodegeneration remains unknown.' is not correct and should be removed. There is a wealth of information on tau-based pathomechanisms available and several studies have identified proteins which become, as seems to be the case for LSD1, trapped by tau in the cytosol.

    Significance

    This form asks me about my expertise. I am working on tau pathomechanisms since more than two decades and the revision experiments I am asking for is what we are doing in our own studies. I find the data on LSD1 interesting, but definitely more work needs to be done to substantiate the claims.

  3. Note: This preprint has been reviewed by subject experts for Review Commons. Content has not been altered except for formatting.

    Learn more at Review Commons


    Referee #2

    Evidence, reproducibility and clarity

    The manuscript "The inhibition of LSD1 via sequestration contributes to tau-mediated neurodegeneration" by Amanda K. Engstrom, Alicia C. Walker, Rohitha A. Moudgal, Dexter A. Myrick, Stephanie M. Kyle and David J. Katz, is an excellent study that beautifully describes the implication of the epigenetic enzyme LSD1, as downstream mediator of tau pathology in neurodegenerative disease.

    The same authors in a previous paper showed that i) loss of LSD1 in the adult mouse brain, leads to significant neuronal cell death and ii) loss of LSD1 induces genome-wide expression changes that significantly overlap with those observed in the brains of postmortem human AD. In this work, are presented initial evidences that in AD brain, LSD1 nuclear function could be disrupted by mislocalization to pathological tau.

    In the present work, using the PS19 mouse model, the authors provide the first cytological evidence that pathological tau can prevent LSD1 from properly localizing to the nucleus in hippocampal and cortical neurons. These data are very strong, the effect is impressive. Crossing the PS19 mouse model of taupathology with a mouse model of LSD1 brain heterozygosity LSD1Δ /+, the authors provide functional data that the inhibition of LSD1 function contributes to tau induced neurodegeneration. Indeed, several pathological parameters measured in the PS19 mouse model, are exacerbated in a reduced genetic LSD1 background. Survival rate, motor activity measured with a rotarod test. The behavioral analysis is nicely paralleled by the analysis of spinal cord motor neurons, showing abnormal morphology in the double mutant mice, compared to the PS19. Overall morphology of the hippocampus shows decreased brain size and brain weight. The analysis is accompanied by MRI analysis, showing again very impressive results, with the double mutant being the most affected and the LSD1Δ /+ very similar to WT.

    The second part of the work is aimed at demonstrating specificity of the functional interaction between tau pathology and LSD1. The authors provide a very well planned transcriptional profiling of the different mouse models, choosing the most relevant time point (prior the onset of neuronal cell death), very clearly justifying the rational of their choice. The data are very convincing, and provide a strong molecular base showing a tight overlap in the effected molecular pathways associated with both pathological tau and Lsd1 heterozygosity. As final approach, the authors rescue neurodegeneration in the hippocampus of PS19 Tau mice overexpressing LSD1 using a neuron-specific virus. Overall, these data establish LSD1 as a major downstream effector of tau-mediated neurodegeneration indicating that the LSD1 pathway is a potential late stage target for intervention in tauopathies, such as AD.

    Minor point:

    In material and Methods is missing a section dedicated to a detailed description of statistical analysis.

    Significance

    I believe that this work will be of great interest for the neurodegenerative together with the neuro-epigenetic field (my personal area of expertise). The identification of a clear new pathway implicated in AD and neurodegeneration together with the suggestion of a possible new therapeutic target (disruption of tau-LSD1 interaction) is of high potential impact for future studies.

  4. Note: This preprint has been reviewed by subject experts for Review Commons. Content has not been altered except for formatting.

    Learn more at Review Commons


    Referee #1

    Evidence, reproducibility and clarity

    This is a very interesting study that addresses an important topic. In brief, the authors build on their previous data showing that LSD1 seems to be neuroprotective. Here they follow the hypothesis that Tau-dependent sequestration of LSD1 to the cytoplasm leads to loss of nuclear LSD1 function. Crossing Tau mutant mice (PS19) to heterozyous LSD1 knock out mice exacerbates phenotypes in PS19 mice, while viral overexpression of LSD1 rescues part of these phenotypes.

    As said the data is interesting but lack mechanistic explanation that would allow in my view publication in a very high profile journal. Moreover, there are some data such as the RNA-seq that would not be acceptable in the present for by any journal. However, all of these issues could be addressed by the authors in case reviewers would refer to them.

    Here are some specific issues.

    1 . Especially the proposed link of Tau-mediated sequestration of LSD1 to the cytoplasm is not fully supported by the data. A key finding shows that LSD1 is seen more in cytoplasm in PS19 mice. However, the biological relevance of this observation cannot be fully appreciated at present, since the magnitude of this phenotype is unclear. Approaches to perform a quantitative analysis in addition to the representative IHC images would be helpful.

    2 . Point 1 might be of specific importance since the subsequent experiments built on the idea that mice with already recued LSD1 levels should have a more severe phenotype in case of Tau pathology. However, they do not really address the role of Tau-mediated sequestration of LSD1 anymore. The authors employ mice that constitutively lack one allele of LSD1 which generally leads to a more severe phenotype in PS19 mice. This is very interesting, but I wonder if reduced LSD1 levels might generally put the network in a more vulnerable state and that other detrimental stimuli that do not cause intracellular protein aggregation might have a similar effect. The authors realize this and address this question by comparing via RNA-seq the gene-expression changes observed in Lsd1+/+, Lsd1Δ/+, PS19 Tau, and PS19;Lsd1Δ/+ littermates. Comparatively few changes are observed. However, the major issue with this experiment is that an n=2/group is simply no acceptable anymore to be published in any serious journal. Thus, this data is not interpretable as it stands.

    Significance

    The data will be interesting to the field and help to further understand the role of LSD1 in neuroegenerative dieases linked to tauopathy.