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TFEB–vacuolar ATPase signaling regulates lysosomal function and microglial activation in tauopathy

Nature Neuroscience volume 27, pages 48–62 (2024)Cite this article

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Abstract

Transcription factor EB (TFEB) mediates gene expression through binding to the coordinated lysosome expression and regulation (CLEAR) sequence. TFEB targets include subunits of the vacuolar ATPase (v-ATPase), which are essential for lysosome acidification. Single-nucleus RNA sequencing of wild-type and PS19 (Tau) transgenic mice expressing the P301S mutant tau identified three unique microglia subclusters in Tau mice that were associated with heightened lysosome and immune pathway genes. To explore the lysosome–immune relationship, we specifically disrupted the TFEB–v-ATPase signaling by creating a knock-in mouse line in which the CLEAR sequence of one of the v-ATPase subunits, Atp6v1h, was mutated. CLEAR mutant exhibited a muted response to TFEB, resulting in impaired lysosomal acidification and activity. Crossing the CLEAR mutant with Tau mice led to higher tau pathology but diminished microglia response. These microglia were enriched in a subcluster low in mTOR and HIF-1 pathways and were locked in a homeostatic state. Our studies demonstrate a physiological function of TFEB–v-ATPase signaling in maintaining lysosomal homeostasis and a critical role of the lysosome in mounting a microglia and immune response in tauopathy and Alzheimer’s disease.

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Fig. 1: Elevated TFEB and lysosomal pathway in PS19 (Tau) mice and by insoluble tau.
Fig. 2: snRNA-seq revealed lysosome and immune pathway upregulation in microglia of Tau mice.
Fig. 3: Shift of microglia subclusters in Tau mice.
Fig. 4: Generation of an in vivo model of lysosomal dysfunction through CLEAR mutagenesis.
Fig. 5: Increased phospho-tau and decreased gliosis in Tau mice crossed to CL background.
Fig. 6: Disruption of TFEB–v-ATPase lysosomal signaling leads to impaired microglia morphology and activation.
Fig. 7: snRNA-seq analysis identified a distinct homeostatic microglia subcluster regulated by TFEB–v-ATPase.
Fig. 8: Disruption of TFEB–v-ATPase regulation leads to compromised lysosomal and inflammatory changes and reduced mTOR and HIF-1 signaling in tauopathy.

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Data availability

Bulk hippocampus RNA-seq and snRNA-seq data generated in this study have been deposited in the GEO with accession number: GSE218728. Public TFEB ChIP-seq in THP1 cell line was downloaded from NCBI with the accession number GSE217608. Any additional information on sequencing data reported in this paper is available upon request. Source data are provided with this paper.

Code availability

The scripts for snRNA-seq and bulk RNA-seq analysis were deposited at https://github.com/qicy2014/snRNA_bulkRNAseq.git.

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Acknowledgements

We are grateful to the Baylor College of Medicine Knockout Mouse Phenotyping Program (KOMP2) and the Genetically Engineered Rodent Models Core for the creation of CL and VKO mice and Cytometry and Cell Sorting Core for FACS analysis. We thank A. Cole, B. Reeves and B. Contreras for expert technical support and members of the Zheng laboratory for stimulating discussions. H.L. is a CPRIT Scholar in Cancer Research (RR200063). This study was supported by grants from the NIH (P01 AG066606, RF1 NS093652, RF1 AG020670 and RF1 AG062257 to H.Z. and R00 AG062746 to H.L.) and CureAlz Fund (to H.Z.).

Author information

Author notes

  1. Heidi Martini-Stoica

    Present address: Department of Otolaryngology, University of North Carolina School of Medicine, Chapel Hill, NC, USA

  2. Yin Xu

    Present address: School of Mental Health and Psychological Sciences, Anhui Medical University, Anhui, China

  3. Marco Sardiello

    Present address: Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA

  4. These authors contributed equally: Baiping Wang, Heidi Martini-Stoica, Chuangye Qi.

Authors and Affiliations

  1. Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA

    Baiping Wang, Heidi Martini-Stoica, Chuangye Qi, Tzu-Chiao Lu, Shuo Wang, Wen Xiong, Yanyan Qi, Yin Xu, Hongjie Li & Hui Zheng

  2. Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA

    Baiping Wang, Marco Sardiello, Hongjie Li & Hui Zheng

  3. Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA

    Heidi Martini-Stoica

  4. Dan and Jan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX, USA

    Marco Sardiello

  5. Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA

    Hui Zheng

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Contributions

B.W., H.M.-S. and H.Z. conceived the project. M.S. and H.L. provided input and expertise in CL mutagenesis and snRNA-seq respectively. H.M.-S. performed bulk brain RNA-seq, created CL mice and was responsible for initial set of cell and mouse experiments. B.W. carried out follow-up molecular, cellular and biochemical analyses and worked with C.Q., T.-C.L., Y.Q. and H.L. in the snRNA-seq experiments and data analysis. S.W. assisted in mouse breeding and biochemical analysis, W.X. constructed acidic nanoparticles and Y.X. performed the seeding experiment. B.W., H.M.-S. and C.Q. prepared the figures, and B.W. and H.Z. wrote the manuscript. All authors read, edited and approved the final manuscript.

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Correspondence to Hui Zheng.

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Extended data

Extended Data Fig. 1 Lysosomal and immune pathway genes are enriched in 9-month-old Tau mice.

a, b. Volcano plots showing differentially expressed genes (DEGs) in Tau mice compared with WT mice at 4 and 9 months of age, respectively. Sample information, raw and unique mapped reads are shown in Supplementary Table 1. c, d. Snapshots of genome browser tracks of bulk brain RNA-seq of WT and Tau mice at 4 or 9 months at the Ctsd loci. e, f. qPCR analysis of hippocampal samples showing TFEB and TFEB regulated lysosomal genes are upregulated in 9 month-old but not 4 month-old Tau mice. Data are presented as average ± SEM. Two-tailed Student’s t-test. N = 4 samples/group for (e). In (f), N = 4 samples/group (Tfeb, Mucoln, Ctsb) and N = 5 samples/group (Ctsd, Ctsa, Lamp1).

Extended Data Fig. 2 snRNA-seq characterization of microglia subtypes.

a. UMAP plots of 55,254 cells from hippocampus of WT and Tau mice after batch effect corrections including batch, sex and genotype. b. UMAP representation of reclustered microglia from WT and Tau mice analyzed by snRNA-seq. The expression levels of homeostatic microglia genes (P2ry12, Ccr5 and Siglech), disease-associated-microglia genes (Apoe, Axl and Csf1) and IFN responsive-microglia genes (Oasl2, Ifi204 and Ifi207) are displayed. Sample information, mean UMI per cell and cell number per library are shown in Supplementary Table 2.

Extended Data Fig. 3 Atp6v1h gene promoter contains strong TFEB binding sites with two tandem CLEAR sequences.

Snapshots of normalized TFEB ChIP-Seq at locus of TFEB targets (ATP6V1H, ATP6V1B2, ATP6V1C1, ATP6V1G1, ATP6V1F, ATP6V0D1, ATP6V1E1, ATP6V0C, ATP6V1A, ATP6V1D). TFEB peaks are highlighted in orange box. CLEAR motifs which are zoomed-in within TFEB binding sites are marked by black lines.

Extended Data Fig. 4 Atp6v1h heterozygous deletion does not affect lysosomal acidification or degradative capacity.

a. qPCR analysis of Atp6v1h transcripts in 9-month-old hippocampal tissues of WT and Atp6v1h heterozygous knockout (VKO). N = 4/group. b. Western blot with quantification of ATP6V1H protein levels in forebrain lysates of 9-month-old WT and VKO mice. N = 3/group. c. Representative images of LysoSensor Green DND-189 fluorescence in WT and VKO primary glial cultures. Bafilomycin (Baf) and NH4Cl treated WT cultures were used as controls. Scale bar: 10 µm. d. Quantification of (c) showing comparable levels of lysosomal acidification in VKO and WT cultures. N = 8 (WT; VKO); N = 6 (Baf); N = 7 (NH4CL). e. Representative images of DQ-BSA fluorescence co-stained with LAMP1 in WT and VKO primary glial cultures. Bafilomycin (Baf) treated WT cultures were used as a control. Scale bar: 10 µm. f. Quantification of (e) showing normal lysosomal degradation capacity in VKO cultures. N = 10/group. Data are presented as average ± SEM. Two-tailed t-test (a,b) and one-way ANOVA with Sidak’s correction (d,f).

Source data

Extended Data Fig. 5 Reduced astrogliosis in Tau;CL mice.

Representative fluorescent confocal images of GFAP and AT8 immunostaining (a) with quantification (b) in the dentate gyrus of 9-month-old Tau and Tau;CL mice. Scale bar: 50 µm and 25 µm in brackets. N = 9/group. Data are presented as average ± SEM. Two-tailed Student’s t-test.

Extended Data Fig. 6 Atp6v1h heterozygous deletion does not affect tau histopathology or gliosis.

a. Representative fluorescent confocal images of AT8, Iba1 and GFAP in the dentate gyrus of 9-month-old WT, VKO, Tau and Tau;VKO. Scale bar: 50 μm. N = 8/group. b–d. Quantification of (a). e. Representative MCI fluorescent confocal images in the dentate gyrus of 9-month-old Tau and Tau;VKO mice. Scale bar: 50 μm. N = 8/group. f. Quantification of (e). g, h. Western blot (g) with quantification (h) of total and phospho-tau species recognized by CP13 and PHF1antibodies. Samples were derived from forebrain lysates of 9-month-old WT, VKO, Tau and Tau;VKO. N = 5/group. i,j. qPCR analysis of Tnfa and Il1b in 9-month-old WT, VKO, Tau and Tau;VKO hippocampal tissues. N = 4 (WT and VKO); N = 5 (Tau and Tau;VKO). Data are presented as average ± SEM. Two-tailed t-test (b,c,d,h,f) and one-way ANOVA with Sidak’s correction (i,j). Tau vs. Tau;VKO: non-significant.

Source data

Extended Data Fig. 7 Acidic nanoparticles are targeted to the lysosomes.

Confocal images showing Acidic nanoparticles (AN) co-localized with Lamp1-marked lysosomes in microglia culture. This experiment was repeated 3 times. Scale bar: 10 µm.

Extended Data Fig. 8 snRNA-seq analysis of hippocampus from WT, Tau, CL and Tau;CL mice.

a. UMAP plots of 137,734 cells from the hippocampus of WT, Tau, CL and Tau;CL mice after batch effect corrections including batch, sex and genotype. b. UMAP plots of 137,734 cells from hippocampus across each genotype. c. UMAP plots of re-clustered microglia cells in female (orange) and male (blue) across genotypes. Sample information, mean UMI per cell and cell number per library are shown in Supplementary Table 2.

Extended Data Fig. 9 Reduced lysosomal and inflammatory pathway genes in Tau;CL microglia.

a. Differentially expressed genes analysis in CL versus WT microglia. Volcano plots showing DEGs for all microglia populations in CL versus WT mice. Up-regulated genes are highlighted in red; Down-regulated genes are highlighted in blue. b. Volcano plots showing DEGs for all microglia in Tau;CL versus WT genotype mice. Up-regulated genes are highlighted in red; Down-regulated genes are highlighted in blue. c. GO enrichment analysis for up-regulated DEGs in Tau;CL vs WT comparing with Tau vs WT. Hypergeometric test was used to identify significant enrichment pathways; FDR < 0.01.

Extended Data Fig. 10 Analysis HIF-1a inhibitor Chrysin treatment in microglia cultures.

a. Representative images of HIF-1α immunofluorescence in primary microglia cultures treated with hypoxia-mimetic CoCl2 alone or co-treated with the HIF-1α inhibitor Chrysin. Scale bar: 20 µm. b. Quantification of (a) showing CoCl2 enhanced HIF-1α protein levels, which were abolished by Chrysin cotreatment. N = 3 independent experiments. c–d. qPCR analysis of the expression of HIF-1α downstream target genes Vegf and Pgk1. N = 3 independent experiments. Data are presented as average ± SEM. One-way ANOVA with Sidak’s correction (b,c,d).

Supplementary information

Source data

Source Data Fig. 4

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Source Data Fig. 5

Unprocessed Western Blots.

Source Data Extended Data Fig. 4

Unprocessed Western Blots.

Source Data Extended Data Fig. 6

Unprocessed Western Blots.

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Wang, B., Martini-Stoica, H., Qi, C. et al. TFEB–vacuolar ATPase signaling regulates lysosomal function and microglial activation in tauopathy. Nat Neurosci 27, 48–62 (2024). https://doi.org/10.1038/s41593-023-01494-2

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