Journal: Nature Communications

Article Title: Microglia-specific regulation of lipid metabolism in Alzheimer’s disease revealed by microglial depletion in 5xFAD Mice

doi: 10.1038/s41467-025-64161-z

Figure Lengend Snippet: A Experimental timeline and interventions. Left: Pharmacological microglial depletion in non-transgenic (Non-Tg) and 5xFAD transgenic mice (mixed B6SJL background) using short-term (2-week) or long-term (3.5 months) treatment. Right: Genetic microglial ablation (FIRE) in 5xFAD mice (B6 background). OSD OpenStandard Diet (Research Diets). Brain samples were collected at indicated time points and analyzed by shotgun lipidomics, NanoString Glial Profiling Panel, and immunofluorescence. Schematic created in BioRender. Xu, Z. (2025) https://BioRender.com/6dlymhx . B –J Pathological characterization after long-term intervention. Representative images and quantifications of microglial marker (P2Y12) ( B –D ), amyloid beta (Aβ, MOAB-2) ( E –G ), and astrocytic marker (GFAP) ( K –M ) immunofluorescence, as well as Methoxy-X04 ( H –J ) fluorescent staining for fibrillar β-sheet amyloid plaques. Each data point represents a brain section, two sections from 3–4 female mice/group were quantified. BZ-X800 Analyzer auto function was used to set a threshold for each section. Representative images shown at matched magnifications and thresholds. N –P APP and neuronal levels. Western blot analysis of APP using 6E10 antibody and synaptic marker Homer1 ( N ), with corresponding quantifications displayed in panels ( O ) and ( P ), respectively. Each data point represents one animal, n = 4–5 mice/group. Trem2 mRNA quantification in both long-term pharmacological ( Q ) and ( R ) genetic cohorts. Each data point represents one animal, n = 4–6 mice/group. All data presented as mean ± SEM. Statistical analysis was performed in GraphPad using one-way ANOVA with Tukey’s post-hoc correction. Representative images (indicated by stars in the corresponding dot plots) were chosen from brain sections present on the same slide, with each slide containing sections from each experimental group. Scale bars: 50 μm for main panels ( B – K ); 20 μm for insets.

Article Snippet: 5xFAD mice (Tg(APPSwFlLon,PSEN1*M146L*L286V)6799Vas/Mmjax), were obtained from the Mutant Mouse Resource and Research Center (MMRRC) at The Jackson Laboratory in two different genetic backgrounds (B6SJL: MMRRC_034840-JAX; and C57BL6: MMRRC_034848-JAX).

Techniques: Transgenic Assay, Immunofluorescence, Marker, Staining, Western Blot

Journal: Nature Communications

Article Title: Microglia-specific regulation of lipid metabolism in Alzheimer’s disease revealed by microglial depletion in 5xFAD Mice

doi: 10.1038/s41467-025-64161-z

Figure Lengend Snippet: A –D Quantification of specific BMP species levels in human postmortem temporal lobe Brodmann area 38 (BA38): comparison of AD vs non-AD controls. Human data normalized by log 10 transformation. Statistical analysis was performed in MetaboAnalyst using metadata table module linear model adjusted for sex and gray/white matter ratio (GWR) with false discovery rate correction for multiple comparisons (FDR = 0.05). E –H Levels of corresponding BMP species in mouse brains following long-term pharmacological microglial depletion. Data normalized by square root transformation and pareto scaling. Statistical analysis was performed in MetaboAnalyst using one-factor module t-testing correcting for multiple comparisons (FDR = 0.05). I –L Levels of same BMP species in mouse brains after genetic microglial depletion. Data normalized by log 10 transformation. Statistical analysis was performed in MetaboAnalyst using metadata table module linear model adjusted for sex correcting for multiple comparisons (FDR = 0.05). Heatmaps of lysosomal gene expression after long-term pharmacological ( M ) and genetic ( N ) microglial depletion. Significantly altered genes denoted: 5xFAD vs Non-Tg (#), and 5xFAD + PLX5622 vs 5xFAD (*) by two-tailed unpaired t-tests with Benjamini-Hochberg correction. Correlations between relative AA-BMP levels and total lysosome gene counts in microglia-depleted mouse brains following long-term pharmacological ( O ) and genetic ( P ) interventions. Statistical analysis was performed in MetaboAnalyst using metadata table module linear model regressing relative AA-BMP levels against all NanoString predefined pathways adjusting for multiple correlations (FDR = 0.05, significance threshold q ≤ 0.05). Each data point represents one animal, n = 4-8 mice/group. All data presented as mean ± SEM.

Article Snippet: 5xFAD mice (Tg(APPSwFlLon,PSEN1*M146L*L286V)6799Vas/Mmjax), were obtained from the Mutant Mouse Resource and Research Center (MMRRC) at The Jackson Laboratory in two different genetic backgrounds (B6SJL: MMRRC_034840-JAX; and C57BL6: MMRRC_034848-JAX).

Techniques: Comparison, Transformation Assay, Gene Expression, Two Tailed Test

Journal: Nature Communications

Article Title: Microglia-specific regulation of lipid metabolism in Alzheimer’s disease revealed by microglial depletion in 5xFAD Mice

doi: 10.1038/s41467-025-64161-z

Figure Lengend Snippet: Relative Grn mRNA expression after long-term pharmacological ( A ) and genetic ( B ) microglial depletion. Correlation analysis of relative AA-BMP levels with relative Grn mRNA expression in long-term pharmacological ( D ) and genetic ( E ) microglial depletion. Relative progranulin protein levels assessed via Western blot ( C ) were correlated with AA-BMP levels ( F ). Each data point represents one animal, n = 4-8 mice/group. Statistical analysis was performed in MetaboAnalyst using metadata table module linear model regressing relative AA-BMP levels against all genes with false discovery rate correction for multiple comparisons (FDR = 0.05). Representative immunofluorescence images showing progranulin (PGRN), Iba1 (microglia/macrophages), MOAB-2 (amyloid plaques) and DRAQ5 (nuclei) in non-Tg ( G ), 5xFAD ( H ) and 5xFAD + PLX5622 ( I ). J Quantification of high progranulin intensity, primarily in plaque-associated and activated microglia. Each data point represents a brain section, 1-2 sections from 3 female mice/group were quantified. All data presented as mean ± SEM, normalized to non-Tg controls. Statistical analysis was performed in GraphPad using ordinary one-way ANOVA with Tukey’s post hoc correction.

Article Snippet: 5xFAD mice (Tg(APPSwFlLon,PSEN1*M146L*L286V)6799Vas/Mmjax), were obtained from the Mutant Mouse Resource and Research Center (MMRRC) at The Jackson Laboratory in two different genetic backgrounds (B6SJL: MMRRC_034840-JAX; and C57BL6: MMRRC_034848-JAX).

Techniques: Expressing, Western Blot, Immunofluorescence

Journal: Alzheimer's & Dementia

Article Title: Degradation of perineuronal nets in hippocampal CA2 explains the loss of social cognition memory in Alzheimer's disease

doi: 10.1002/alz.70813

Figure Lengend Snippet: Progressive disruption of Hippocampal CA2 PNNs in 5XFAD mice. (A) Confocal micrographs showing immunohistochemical expression of WFA (magenta)‐labeled PNNs in coronal half‐brain sections from control and 5XFAD mice. Magnified areas in white rectangles highlight disruption of PNNs around hippocampal CA2 pyramidal neurons labeled with PCP4 (green). Scale 500 µm main images, 50 µm magnified images. (B) High magnification confocal micrographs of a single CA2 pyramidal neuron showing PNN disruption in 5XFAD and consequent loss of characteristic high‐intensity peaks and valley pattern in the line intensity profile (bottom). A line was drawn along the WFA signal in the PCP4 neuron periphery in control and 5XFAD group, showing many high‐intensity WFA peaks in control (dark magenta line) compared to the 5XFAD (light magenta line) group. Scale 2 µm. (C–F) Representative confocal micrographs of PNN (WFA‐magenta) immunofluorescence associated with CA2 pyramidal neurons (PCP4‐green) in 5XFAD mice at 3 (C), 6 (D), 9 (E), and 12 M (F) groups showing progressive PNN loss. Scale 50 µm. (G–H) Bar graphs of CA2 PNN area coverage (WFA/PCP4 area) (G), and CA2 PNN (WFA) intensity (H) in 5XFAD and their age‐matched control mice at 3, 6, 9, and 12 M showing significant decreases at and after 6 M in 5XFAD; n = 7–8 slices from five mice per group in 3 M, n = 9–10 brain slices from five mice per group in 6 M, n = 9–10 brain slices from five mice per group in 9 M, n = 10–12 brain slices from five mice per group in 12 M. (I–J) PV neuron density (I), and NeuN neuron density (J) in CA2 area at 3 and 6 M 5XFAD mice compared to their age‐matched controls showing no difference between any groups; n = 8–9 brain slices from five mice per group in 3 M, n = 9–10 brain slices from five mice per group in 6 M. Bar data in G–H indicate mean ± SEM and dots represent data points. Two‐way ANOVA, Tukey's multiple comparisons test in G–H; unpaired two‐tailed t ‐test in I–J. * p < 0.05, ** p < 0.01, *** p < 0.001,**** p < 0.0001, and ns p > 0.05.

Article Snippet: We obtained 5XFAD mice (B6SJL‐Tg (APPSwFlLon, PSEN1*M146L*L286V) 6799Vas/ Mmjax, strain 034840‐JAX) from the Jackson Laboratory and backcrossed for five generations to C57Bl/6J (000664‐JAX) wild‐type (WT) mice to obtain an incipient congenic line on a C57Bl/6J genetic background for experiments.

Techniques: Disruption, Immunohistochemical staining, Expressing, Labeling, Control, Immunofluorescence, Two Tailed Test

Journal: Alzheimer's & Dementia

Article Title: Degradation of perineuronal nets in hippocampal CA2 explains the loss of social cognition memory in Alzheimer's disease

doi: 10.1002/alz.70813

Figure Lengend Snippet: Impairment of social memory in 5XFAD mice at 6 M age. (A) Schematic of the direct interaction social memory test. The test mouse (red dot) interacts with Novel 1 mouse (yellow dot) who becomes Familiar (yellow dot) in the second trial. In the following trial, the test mouse (red dot) interacts with another novel (Novel 2) mouse (green dot). (B) Graph showing time spent investigating by 3 M old 5XFAD and age‐matched control mice with Novel 1, Familiar, and Novel 2 mice suggesting normal social memory (two‐way repeated measures ANOVA, Tukey's multiple comparisons test ( n = 7) (control); 9 (5XFAD) mice; * p < 0.05, *** p < 0.001). (C–D) Bar graphs showing no significant change in difference scores, (C) Novel 1 – Familiar, and (D) Familiar − Novel 2, in 3 M 5XFAD mice compared to age‐matched control mice ( n = 7) (control); 9 (5XFAD) mice in (C–D), unpaired two‐tailed t ‐test. (E) Graph showing impaired social memory in 6 M 5XFAD mice compared to 6 M control mice ( n = 10) (control); 9 (5XFAD) mice, two‐way repeated measures ANOVA, Tukey's multiple comparisons test; * p < 0.05, **** p < 0.0001. (F) Bar graph showing significant change in difference scores (Novel 1 − Familiar) in 6 M 5XFAD mice compared to 6 M control mice ( n = 10) (control); 9 (5XFAD) mice; unpaired two‐tailed t ‐test; * p < 0.05. (G) Bar graph showing significant change in difference scores (Familiar − Novel 2) in 6 M 5XFAD mice compared to 6 M control mice ( n = 10) (control); 9 (5XFAD) mice; unpaired two‐tailed t ‐test, ** p < 0.01. (H) Schematic of novel object recognition task. The test mouse is familiarized with two objects (blue), followed by replacing one object with a novel object (green) in the next trial. (I) Bar graph showing significantly higher time spent with the novel object compared to familiar by both 6 M control and 5XFAD ( n = 11) (control); 17 (5XFAD) mice, two‐way ANOVA mixed‐effects Šídák's; ** p < 0.01. (J–K) Bar graph showing no significant difference in discrimination index (J), and distance moved (K) by both 6 M control and 5XFAD ( n = 11) (J), 17 (K) control; 17 (J), 22 (K) 5XFAD mice; unpaired two‐tailed t ‐test.

Article Snippet: We obtained 5XFAD mice (B6SJL‐Tg (APPSwFlLon, PSEN1*M146L*L286V) 6799Vas/ Mmjax, strain 034840‐JAX) from the Jackson Laboratory and backcrossed for five generations to C57Bl/6J (000664‐JAX) wild‐type (WT) mice to obtain an incipient congenic line on a C57Bl/6J genetic background for experiments.

Techniques: Control, Two Tailed Test

Journal: Alzheimer's & Dementia

Article Title: Degradation of perineuronal nets in hippocampal CA2 explains the loss of social cognition memory in Alzheimer's disease

doi: 10.1002/alz.70813

Figure Lengend Snippet: Transcriptomic analysis of age‐dependent CA2 area gene expression changes in 5XFAD mice. (A) Schematic of experimental design. We tested social memory in 3 and 7 M old control and 5XFAD mice followed by acute brain slicing and isolation of the CA2 area using a tissue puncher. CA2 area tissues were frozen fixed and processed for bulk RNA‐sequencing. (B) Volcano plot showing DEGs in the CA2 area in 3 M 5XFAD and age‐matched control mice. Genes with an adjusted p ‐value < 0.05 are shown in blue, genes with log 2 fold‐change > 1.00 in green, and genes meeting both criteria in red. Gray dots represent genes that do not meet either criterion. (C) Volcano plot showing DEGs in the CA2 area in 7 M 5XFAD and age‐matched control mice. Color coding is consistent with that in (B). (D–E) GO term circle plot highlighting the top 10 GO terms, sorted by adjusted p ‐value in (D) 3 M, and (E) 7 M, 5XFAD versus age‐matched control mice. Z‐scores indicate the directionality of regulation, with red reflecting upregulated genes and blue reflecting downregulated genes. (F, G) GO term circle plot of the top 10 GO terms related to PNNs and ECM, ranked by adjusted p ‐value. Z‐scores indicate the directionality of regulation, with red reflecting upregulated genes. (H–I) Heatmaps showing the expression levels of key genes involved in, (H) PNN synthesis, and (I) PNN degradation across all samples and experimental conditions. Expression values were normalized by z‐score transformation.

Article Snippet: We obtained 5XFAD mice (B6SJL‐Tg (APPSwFlLon, PSEN1*M146L*L286V) 6799Vas/ Mmjax, strain 034840‐JAX) from the Jackson Laboratory and backcrossed for five generations to C57Bl/6J (000664‐JAX) wild‐type (WT) mice to obtain an incipient congenic line on a C57Bl/6J genetic background for experiments.

Techniques: Gene Expression, Control, Isolation, RNA Sequencing, Expressing, Transformation Assay

Journal: Alzheimer's & Dementia

Article Title: Degradation of perineuronal nets in hippocampal CA2 explains the loss of social cognition memory in Alzheimer's disease

doi: 10.1002/alz.70813

Figure Lengend Snippet: The MMP blocker GM6001 delays social memory deficits and inhibits PNN degradation in 5XFAD mice. (A) Schematic of experimental design. We assessed social memory in 5 M 5XFAD and age‐matched control mice followed by i.p. GM6001 or vehicle injections for 1 month. Mice were again assessed for social memory after the injections and brains were collected for IHC. (B) Graph showing normal social memory in 5 M 5XFAD and age‐matched control mice ( n = 7) (control), 11 (5XFAD) mice; two‐way ANOVA, Tukey's multiple comparisons test; * p < 0.05, ** p < 0.01. (C–D) Bar graphs showing no significant change in difference scores, (C) Novel 1 – Familiar, and (D) Familiar − Novel 2, in 5 M 5XFAD mice compared to age‐matched control mice ( n = 7) (control); 11 (5XFAD) mice in (C–D), unpaired two‐tailed t ‐test. (E) Graph showing normal social memory in a month‐long GM6001‐injected 6 M 5XFAD mice whereas vehicle‐injected 6 M 5XFAD mice show disrupted social memory compared to the age‐matched control mice ( n = 14) (5XFAD + GM6001), 12 (5XFAD + vehicle) mice; two‐way ANOVA, Tukey's multiple comparisons test; * p < 0.05, **** p < 0.0001. (F–G) Bar graphs showing significant difference in difference scores (F) Novel 1 – Familiar, and (G) Familiar − Novel 2, in GM6001‐injected 6 M 5XFAD in 6 M compared to vehicle‐injected 6 M 5XFAD mice ( n = 14) (5XFAD + GM6001), 12 (5XFAD + vehicle) mice in (F–G); unpaired two‐tailed t ‐test; *** p < 0.001, **** p < 0.0001. (H) Representative confocal micrographs of PNN (WFA) immunofluorescence in CA2 area (PCP‐4) from 6 M 5XFAD mice injected with vehicle (top), or GM6001 (2nd from top), and 6 M Control (5XFAD‐) mice injected with vehicle (3rd from top) or GM6001 (bottom). Scale 50 µm. (I) Bar graphs showing significantly higher CA2 PNN expression in GM6001‐treated mice compared to vehicle‐treated 5XFAD mice whereas age‐matched GM6001‐treated or vehicle‐treated controls exhibited PNN expression comparable to 6 M GM6001‐treated 5XFAD mice (one‐way ANOVA, Tukey's multiple comparisons test; n = 4–5 mice per group; * p < 0.05, ** p < 0.01).

Article Snippet: We obtained 5XFAD mice (B6SJL‐Tg (APPSwFlLon, PSEN1*M146L*L286V) 6799Vas/ Mmjax, strain 034840‐JAX) from the Jackson Laboratory and backcrossed for five generations to C57Bl/6J (000664‐JAX) wild‐type (WT) mice to obtain an incipient congenic line on a C57Bl/6J genetic background for experiments.

Techniques: Control, Two Tailed Test, Injection, Immunofluorescence, Expressing

Journal: Cells

Article Title: Retinal Degeneration in Alzheimer’s Disease 5xFAD Mice Fed DHA-Enriched Diets

doi: 10.3390/cells15010008

Figure Lengend Snippet: Illustrative representation of the major layers in the retina of 5xFAD mice (magnification of ×100, scale bar = 100 µm).

Article Snippet: Forty five-week-old 5xFAD male mice were acquired from Charles River Laboratories (L’Arbresle, France).

Techniques:

Journal: Cells

Article Title: Retinal Degeneration in Alzheimer’s Disease 5xFAD Mice Fed DHA-Enriched Diets

doi: 10.3390/cells15010008

Figure Lengend Snippet: Measurement of retinal layers thickness (µm) in 5xFAD mice fed DHA-enriched diets. ( A ) total layers; ( B ) inner segment/outer segment layer; ( C ) outer nuclear layer; ( D ) outer plexiform layer; ( E ) inner nuclear layer; ( F ) inner plexiform layer; ( G ) ganglion cell layer; ( H ) nerve fibre layer. No statistically significant differences were found, p > 0.05.

Article Snippet: Forty five-week-old 5xFAD male mice were acquired from Charles River Laboratories (L’Arbresle, France).

Techniques:

Journal: Cells

Article Title: Retinal Degeneration in Alzheimer’s Disease 5xFAD Mice Fed DHA-Enriched Diets

doi: 10.3390/cells15010008

Figure Lengend Snippet: Ganglion cell layer (GCL) density in the retina of 5xFAD mice fed DHA-enriched diets. Different letters indicate statistical significances at p < 0.05.

Article Snippet: Forty five-week-old 5xFAD male mice were acquired from Charles River Laboratories (L’Arbresle, France).

Techniques:

Journal: Cells

Article Title: Retinal Degeneration in Alzheimer’s Disease 5xFAD Mice Fed DHA-Enriched Diets

doi: 10.3390/cells15010008

Figure Lengend Snippet: Illustrative images of immunohistochemical staining against β-amyloid plaques in the retina of 5xFAD mice fed DHA-enriched diets: ( A ) magnification of ×40, scale bar = 200 µm; ( B ) magnification of 200×, scale bar = 50 µm. IS/OS: Inner segment/outer segment layer; ONL: Outer nuclear layer; OPL: Outer plexiform layer; INL: Inner nuclear layer; IPL: Inner plexiform layer; GCL: Ganglion cell layer.

Article Snippet: Forty five-week-old 5xFAD male mice were acquired from Charles River Laboratories (L’Arbresle, France).

Techniques: Immunohistochemical staining, Staining

Journal: Cells

Article Title: Retinal Degeneration in Alzheimer’s Disease 5xFAD Mice Fed DHA-Enriched Diets

doi: 10.3390/cells15010008

Figure Lengend Snippet: Representative immunohistochemical images of TAU staining in the retina of 5xFAD mice fed DHA-enriched diets: ( A ) magnification of ×40, scale bar = 200 µm; ( B ) magnification of 400×, scale bar = 20 µm. Graphical representations for the following: ( C ) TAU count; ( D ) % of TAU staining. ONL: Outer nuclear layer; OPL: Outer plexiform layer; INL: Inner nuclear layer; IPL: Inner plexiform layer. Different letters indicate statistical significances at p < 0.05.

Article Snippet: Forty five-week-old 5xFAD male mice were acquired from Charles River Laboratories (L’Arbresle, France).

Techniques: Immunohistochemical staining, Staining

Journal: Cells

Article Title: Retinal Degeneration in Alzheimer’s Disease 5xFAD Mice Fed DHA-Enriched Diets

doi: 10.3390/cells15010008

Figure Lengend Snippet: Illustrative images of immunohistochemical staining against IBA1 in the retina of 5xFAD mice fed DHA-enriched diets: ( A ) magnification of ×40, scale bar = 200 µm; ( B ) magnification of 200×, scale bar = 50 µm. IS/OS: Inner segment/outer segment layer; ONL: Outer nuclear layer; OPL: Outer plexiform layer; INL: Inner nuclear layer; IPL: Inner plexiform layer; GCL: Ganglion cell layer.

Article Snippet: Forty five-week-old 5xFAD male mice were acquired from Charles River Laboratories (L’Arbresle, France).

Techniques: Immunohistochemical staining, Staining

Journal: Cells

Article Title: Retinal Degeneration in Alzheimer’s Disease 5xFAD Mice Fed DHA-Enriched Diets

doi: 10.3390/cells15010008

Figure Lengend Snippet: Loading plot of the first and second principal components (PCs) of the component score vectors ( A ) and pooled data ( B ) for the measurement of retinal layers thickness, TAU immunohistochemical staining, and ganglion cell layer (GCL) density in the retina of 5xFAD mice fed DHA-enriched diets: control diet; LSO, linseed oil diet; FO, fish oil diet; Schizo, Schizochytrium microalga oil diet; and DHASCO, commercial DHASCO oil diet. Blue circle in panel ( A ) indicates the discrimination of dietary groups.

Article Snippet: Forty five-week-old 5xFAD male mice were acquired from Charles River Laboratories (L’Arbresle, France).

Techniques: Immunohistochemical staining, Staining, Control