DataSheet1_Ontology Specific Alternative Splicing Changes in Alzheimer’s Disease.ZIP

Alternative splicing (AS) is a common phenomenon and correlates with aging and aging-related disorders including Alzheimer’s disease (AD). We aimed to systematically characterize AS changes in the cerebral cortex of 9-month-old APP/PS1 mice. The GSE132177 dataset was downloaded from GEO and ENA databases, aligned to the GRCm39 reference genome from ENSEMBL via STAR. Alternative 3′SS (A3SS), alternative 5′SS (A5SS), skipped exon (SE), retained intron (RI), and mutually exclusive exons (MXE) AS events were evaluated using rMATS, rmats2sashimiplot, and maser. Differential genes or transcripts were analyzed using the limma R package. Gene ontology analysis was performed with the clusterProfiler R package. A total of 60,705 raw counts of AS were identified, and 113 significant AS events were finally selected in accordance with the selection criteria: 1) average coverage >10 and 2) delta percent spliced in (ΔPSI) >0.1. SE was the most abundant AS event (61.95%), and RI was the second most abundant AS type (13.27%), followed by A3SS (12.39%), thereafter A5SS and MXE comprised of 12.39%. Interestingly, genes that experienced SE were enriched in histone acetyltransferase (HAT) complex, while genes spliced by RI were enriched in autophagy and those which experienced A3SS were enriched in methyltransferase activity revealed by GO analysis. In conclusion, we revealed ontology specific AS changes in AD. Our analysis provides novel pathological mechanisms of AD.</p

Table_3_Single-cell RNA sequencing of CSF reveals neuroprotective RAC1+ NK cells in Parkinson’s disease.xlsx

Brain infiltration of the natural killer (NK) cells has been observed in several neurodegenerative disorders, including Parkinson’s disease (PD). In a mouse model of α-synucleinopathy, it has been shown that NK cells help in clearing α-synuclein (α-syn) aggregates. This study aimed to investigate the molecular mechanisms underlying the brain infiltration of NK cells in PD. Immunofluorescence assay was performed using the anti-NKp46 antibody to detect NK cells in the brain of PD model mice. Next, we analyzed the publicly available single-cell RNA sequencing (scRNA-seq) data (GSE141578) of the cerebrospinal fluid (CSF) from patients with PD to characterize the CSF immune landscape in PD. Results showed that NK cells infiltrate the substantia nigra (SN) of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced PD model mice and colocalize with dopaminergic neurons and α-syn. Moreover, the ratio of NK cells was found to be increased in the CSF of PD patients. Analysis of the scRNA-seq data revealed that Rac family small GTPase 1 (RAC1) was the most significantly upregulated gene in NK cells from PD patients. Furthermore, genes involved in regulating SN development were enriched in RAC1+ NK cells and these cells showed increased brain infiltration in MPTP-induced PD mice. In conclusion, NK cells actively home to the SN of PD model mice and RAC1 might be involved in regulating this process. Moreover, RAC1+ NK cells play a neuroprotective role in PD.</p

Table_1_Single-cell RNA sequencing of CSF reveals neuroprotective RAC1+ NK cells in Parkinson’s disease.xlsx

Brain infiltration of the natural killer (NK) cells has been observed in several neurodegenerative disorders, including Parkinson’s disease (PD). In a mouse model of α-synucleinopathy, it has been shown that NK cells help in clearing α-synuclein (α-syn) aggregates. This study aimed to investigate the molecular mechanisms underlying the brain infiltration of NK cells in PD. Immunofluorescence assay was performed using the anti-NKp46 antibody to detect NK cells in the brain of PD model mice. Next, we analyzed the publicly available single-cell RNA sequencing (scRNA-seq) data (GSE141578) of the cerebrospinal fluid (CSF) from patients with PD to characterize the CSF immune landscape in PD. Results showed that NK cells infiltrate the substantia nigra (SN) of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced PD model mice and colocalize with dopaminergic neurons and α-syn. Moreover, the ratio of NK cells was found to be increased in the CSF of PD patients. Analysis of the scRNA-seq data revealed that Rac family small GTPase 1 (RAC1) was the most significantly upregulated gene in NK cells from PD patients. Furthermore, genes involved in regulating SN development were enriched in RAC1+ NK cells and these cells showed increased brain infiltration in MPTP-induced PD mice. In conclusion, NK cells actively home to the SN of PD model mice and RAC1 might be involved in regulating this process. Moreover, RAC1+ NK cells play a neuroprotective role in PD.</p

Table_2_Single-cell RNA sequencing of CSF reveals neuroprotective RAC1+ NK cells in Parkinson’s disease.xlsx

Brain infiltration of the natural killer (NK) cells has been observed in several neurodegenerative disorders, including Parkinson’s disease (PD). In a mouse model of α-synucleinopathy, it has been shown that NK cells help in clearing α-synuclein (α-syn) aggregates. This study aimed to investigate the molecular mechanisms underlying the brain infiltration of NK cells in PD. Immunofluorescence assay was performed using the anti-NKp46 antibody to detect NK cells in the brain of PD model mice. Next, we analyzed the publicly available single-cell RNA sequencing (scRNA-seq) data (GSE141578) of the cerebrospinal fluid (CSF) from patients with PD to characterize the CSF immune landscape in PD. Results showed that NK cells infiltrate the substantia nigra (SN) of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced PD model mice and colocalize with dopaminergic neurons and α-syn. Moreover, the ratio of NK cells was found to be increased in the CSF of PD patients. Analysis of the scRNA-seq data revealed that Rac family small GTPase 1 (RAC1) was the most significantly upregulated gene in NK cells from PD patients. Furthermore, genes involved in regulating SN development were enriched in RAC1+ NK cells and these cells showed increased brain infiltration in MPTP-induced PD mice. In conclusion, NK cells actively home to the SN of PD model mice and RAC1 might be involved in regulating this process. Moreover, RAC1+ NK cells play a neuroprotective role in PD.</p

DataSheet_1_Single-cell RNA sequencing of CSF reveals neuroprotective RAC1+ NK cells in Parkinson’s disease.pdf

Brain infiltration of the natural killer (NK) cells has been observed in several neurodegenerative disorders, including Parkinson’s disease (PD). In a mouse model of α-synucleinopathy, it has been shown that NK cells help in clearing α-synuclein (α-syn) aggregates. This study aimed to investigate the molecular mechanisms underlying the brain infiltration of NK cells in PD. Immunofluorescence assay was performed using the anti-NKp46 antibody to detect NK cells in the brain of PD model mice. Next, we analyzed the publicly available single-cell RNA sequencing (scRNA-seq) data (GSE141578) of the cerebrospinal fluid (CSF) from patients with PD to characterize the CSF immune landscape in PD. Results showed that NK cells infiltrate the substantia nigra (SN) of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced PD model mice and colocalize with dopaminergic neurons and α-syn. Moreover, the ratio of NK cells was found to be increased in the CSF of PD patients. Analysis of the scRNA-seq data revealed that Rac family small GTPase 1 (RAC1) was the most significantly upregulated gene in NK cells from PD patients. Furthermore, genes involved in regulating SN development were enriched in RAC1+ NK cells and these cells showed increased brain infiltration in MPTP-induced PD mice. In conclusion, NK cells actively home to the SN of PD model mice and RAC1 might be involved in regulating this process. Moreover, RAC1+ NK cells play a neuroprotective role in PD.</p

Additional file 1 of N6-methyladenosine-modified circRIMS2 mediates synaptic and memory impairments by activating GluN2B ubiquitination in Alzheimer's disease

Additional file 1: Fig. S1. circRIMS2 functions as a miRNA sponge of miR-3968. Fig. S2. METTL3 mediated m6A modification of circRIMS2. Fig. S3. Downstream target validation of miR-3968. Fig. S4. Overexpression of miR-3968 or silencing UBE2K rescues circRIMS2 induced memory impairment and synaptic disorders in vivo. Fig. S5. GluN2B-2 interacted with UBE2K. Fig. S6. Injection of control lentivirus did not affect the learning and memory of WT mice. Fig. S7. METTL3 did not affect the m6A modification of UBE2K and GluN2B. Fig. S8. Silencing METTL3 reversed the m6A level of circRIMS2 in APP/PS1 mice. Table S1. List of the primary and secondary antibodies. Table S2. The dysregulated circRNAs in the hippocampus of 4-month-old APP/PS1 mice. Table S3. The dysregulated miRNAs in the hippocampus of 4-month-old APP/PS1 mice. Table S4. The predicted circRNA/miRNA ceRNA pairs by miRanda. Table S5. The predicted targets of miR-3968

Additional file 1 of A novel transgenic mouse line with hippocampus-dominant and inducible expression of truncated human tau

Additional file 1: Fig. S1. Generation and genomic identification of hTau368 mice. Fig. S2. hTau368 had predominantly expression in hippocampus, slightly in other regions. Fig. S3. Reversible tau phosphorylation in hTau368 mice following dox-off. Fig. S4. Dox treatment increased hTau in the pan-cortex of hTau368 mice. Fig. S5. Dox-treated hTau368 mice showed enhanced Gallyas silver staining in DG granular cells, although the staining intensity was much slighter than that detected in the brain slice of AD patients. Fig. S6. Dox-treated hTau368 mice did not show amyloid deposition. Fig. S7. Dox treatment upregulated GSK-3β activity in the hippocampus of hTau368 mice. Fig. S8. Enhanced gliosis in entorhinal-piriform cortex of dox-treated hTau368 mice. Fig. S9. Dox treatment showed limited effect on glia activation in wild-type mice. Fig. S10. Reduction of tau correlates with increased synapse-associated proteins in hTau368 mice. Fig. S11. The loss of hippocampal neurons ceased when dox was retracted for hTau368 mice. Fig. S12. Dox-treated hTau368 mice tended to exhibit increased locomotor activities. Fig. S13. hTau368 mice showed no gender difference in tauopathy and cognitive behaviors. Table S1. Primers used for the identification of hTau368 mice. Table S2. Antibodies used in this study

Additional file 1 of Targeting a vulnerable septum-hippocampus cholinergic circuit in a critical time window ameliorates tau-impaired memory consolidation

Additional file 1: sFigure 1. Accumulation of hyperphosphorylated tau is remarkably increased in the medial septum (MS) of AD mouse models. (A-B) Representative images showing prominent accumulation of phosphorylated tau (pT205 and pT231) in the MS of 9-month 3xTg AD mice (A) and 5xFAD mice (B) measured by immunofluorescence staining. N = 3 mice per group. Scale bar, 50 μm

Additional file 2 of Targeting a vulnerable septum-hippocampus cholinergic circuit in a critical time window ameliorates tau-impaired memory consolidation

Additional file 2: sFigure 2. Molecular characterization of cholinergic neurons in the MS. (A, D) Representative images show co-localization of ChAT with CaMKII or GABA by co-immunofluorescence staining. (B, C, E, F) Quantitative analyses showed that ~93% and ~28% of ChAT+ neurons were respectively co-stained with CaMKII and GABA, while ~13% CaMKII+ and ~7% GABA+ neurons were respectively ChAT. N = 6 mice per group. Scale bar, 50 μm

Additional file 3 of Targeting a vulnerable septum-hippocampus cholinergic circuit in a critical time window ameliorates tau-impaired memory consolidation

Additional file 3: sFigure 3. Overexpressing hTau in CaMKII neuron does not induce spatial cognitive deficit or anxiety-related behaviors. (A, B) Overexpression of exogenous hTau in the CaMKII+ neurons of MS by infusion of AAV-CaMKII-Cre-mCherry and AAV-DIO-hTau/vector-EGFP, and ~95% of hTau were colocalized with CaMKII. N = 6 mice per group. Scale bar, 20 μm. (C-H) Three months after hTau overexpression, MS-CaMKII-hTau mice showed comparable spatial learning (C, D) and memory (E-H) with controls in BM test. During spatial learning trials, no differences of latency (C, two–way ANOVA group × days, escape latency: F [3,64] = 0.1376, P > 0.05) and number of errors (D, two–way ANOVA group × days, number of errors: F [3,64] = 0.11117, P > 0.05) were found between MS-CaMKII-hTau mice and the controls. In probe test, latency (E, unpaired t test, t = 0.7425 df = 16, P > 0.05), %correct poke (F, unpaired t test, t = 0.9169 df = 16, P > 0.05), %time in target (G, unpaired t test, t = 0.4458 df = 16, P > 0.05) and distance moved (H, unpaired t test, t = 0.01734 df = 16, P > 0.05) in MS-CaMKII-hTau group were identical to the controls. (I-N) Six months after hTau overexpression, MS-CaMKII-hTau mice displayed normal spatial learning (I, J) and memory (K-N) in BM test. I, two–way ANOVA group × days, escape latency: F [3,64] = 0.1346, P > 0.05; J, two–way ANOVA group × days, number of errors: F [3,64] = 0.3938, P > 0.05; K, unpaired t test, t = 0.5077 df = 16, P > 0.05, L, unpaired t test, t = 0.5866 df = 16, P > 0.05; M, unpaired t test, t = 0.1670 df = 16, P > 0.05 and N, unpaired t test, t = 0.1707 df = 16, P > 0.05. N = 9 mice per group (O-V) Overexpressing hTau in CaMKII+ neurons of MS for 3 or 6 m had no effects on anxiety-related behaviors in elevated plus maze test (O, P, S, T) and open field test (Q, R, U, V). O, unpaired t test, t = 0.5116 df = 18, P > 0.05 [3 m]; P, unpaired t test, t = 0.9208 df = 18, P > 0.05 [3 m]; S, unpaired t test, t = 0.3445 df = 18, P > 0.05 [6 m]; T, unpaired t test, t = 0.03656 df = 18, P > 0.05 [6 m]；Q, unpaired t test, t = 0.4622 df = 18, P > 0.05 [3 m]; R, unpaired t test, t = 0.02165 df = 18, P > 0.05 [3 m]; U, unpaired t test, t = 0.2111 df = 18, P > 0.05 [6 m]; V, unpaired t test, t = 0.2087 df = 18, P > 0.05 [6 m]. N = 10 mice per group. presented as mean ± SEM