surface plasmon resonance spr  (Thermo Fisher)

Journal: Neural Regeneration Research

Article Title: Low-density lipoprotein receptor–related protein 1 mediates α-synuclein transmission from the striatum to the substantia nigra in animal models of Parkinson’s disease

doi: 10.4103/NRR.NRR-D-23-01965

Figure Lengend Snippet: LRP1 expression is increased in the nigrostriatal system of a monkey model of PD induced by α-syn PFFs injection. (A) Clinical rating score of monkeys after stereotactic injection of 600 μg of α-syn PFFs or an equal volume of normal saline for 4 months. (B) Immunohistochemistry detection of TH in the STR (left) and SN (right). The TH signal intensity in the STR and the number of TH-positive neurons in the SN were lower in the PFF group. The black arrow heads indicate typical TH-positive neurons. Scale bars: 100 μm. (C) Quantitative immunohistochemistry density analysis of TH in the STR. (D) Quantitation of the ratio of TH-positive neurons in the SN in the PFF group compared with the Sham group. (E) Western blot analysis of TH, LRP1, and α-syn expression levels in the monkey STR. (F–H) Densitometric analysis of TH (F), LRP1 (G), and α-syn (H) expression levels in the STR. (I) Western blot analysis of TH, LRP1, and α-syn expression levels in the monkey SN. (J–L) Densitometric analysis of TH (J), LRP1 (K), and α-syn (L) expression levels in the SN. Data are expressed as mean ± SD ( n = 3). * P < 0.05, ** P < 0.01, *** P < 0.001, vs. Sham group (unpaired t -test). LRP1: Low-density lipoprotein receptor-related protein 1; PD: Parkinson’s disease; PFF: pre-formed fibril; SN: substantia nigra; STR: striatum; TH: tyrosine hydroxylase; α-syn: α-synuclein.

Article Snippet: α-Syn PFFs (SPR-322, StressMarq, Victoria, Canada) were sonicated with a handheld probe (VCX130, SONICS & MATERIALS, Newtown, CT, USA) as follows: amplitude 30% and time 15 seconds (pulse on 3 seconds, pulse off 6 seconds) (Volpicelli-Daley et al., 2014; Sun et al., 2022b).

Techniques: Expressing, Injection, Saline, Immunohistochemistry, Quantitation Assay, Western Blot

Journal: Neural Regeneration Research

Article Title: Low-density lipoprotein receptor–related protein 1 mediates α-synuclein transmission from the striatum to the substantia nigra in animal models of Parkinson’s disease

doi: 10.4103/NRR.NRR-D-23-01965

Figure Lengend Snippet: LRP1 expression is increased in the nigrostriatal system of a mouse model of PD induced by injection with α-Syn PFFs. (A) Visual gait analysis of walking, gait, and footprint pressure in mice after stereotactic injection with 5 μg of α-Syn PFFs or an equal volume of PBS for 4 weeks ( n = 6). (B) Normal step sequence in mice ( n = 6). (C) Average speed in mice ( n = 6). (D) Tripod support time in mice ( n = 6). (E) Immunohistochemistry staining for TH in the STR. The images in the second row are enlarged images of the areas indicated in black boxes in the upper row. The TH signal intensity in the STR was lower in the PFF group. Scale bars: 200 μm, 40 μm (enlarged). (F) Immunohistochemistry staining for TH in the SN. The images in the second row are enlarged images of the areas indicated in black boxes in the upper row, and the white arrowheads indicate typical TH-positive neurons. There were fewer TH-positive neurons in the SN in the PFF group. Scale bars: 100 μm, 20 μm (enlarged). (G) Quantitative immunohistochemistry density analysis of TH in the STR, compared with the Sham group ( n = 3). (H) Quantitation of the ratio of TH-positive neurons in the SN in the PFF group compared with the Sham group ( n = 3). (I) Western blot analysis of TH, LRP1, and α-Syn expression levels in the mouse STR after injection with 5 μg of α-Syn PFFs or an equal volume of PBS ( n = 3). (J–L) Densitometric analysis of TH (J), LRP1 (K), and α-Syn (L) expression levels in the STR. (M) Western blot analysis of TH, LRP1, and α-Syn expression levels in the mouse SN ( n = 3). (N–P) Densitometric analysis of TH (N), LRP1 (O), and α-Syn (P) expression levels in the SN ( n = 3). Data are expressed as mean ± SD ( n = 3). * P < 0.05, ** P < 0.01, *** P < 0.001, vs . Sham group (unpaired t -test). LRP1: Low-density lipoprotein receptor-related protein 1; PBS: phosphate buffered solution; PD: Parkinson’s disease; PFF: pre-formed fibril; SN: substantia nigra; STR: striatum; TH: tyrosine hydroxylase; α-Syn: α-synuclein.

Article Snippet: α-Syn PFFs (SPR-322, StressMarq, Victoria, Canada) were sonicated with a handheld probe (VCX130, SONICS & MATERIALS, Newtown, CT, USA) as follows: amplitude 30% and time 15 seconds (pulse on 3 seconds, pulse off 6 seconds) (Volpicelli-Daley et al., 2014; Sun et al., 2022b).

Techniques: Expressing, Injection, Sequencing, Immunohistochemistry, Staining, Quantitation Assay, Western Blot

Journal: Neural Regeneration Research

Article Title: Low-density lipoprotein receptor–related protein 1 mediates α-synuclein transmission from the striatum to the substantia nigra in animal models of Parkinson’s disease

doi: 10.4103/NRR.NRR-D-23-01965

Figure Lengend Snippet: Exogenous α-syn PFFs upregulate LRP1 expression in PC12 cells. (A) Viability of PC12 cells incubated with different doses (0, 5, 10, 20, or 50 µg/mL) of α-Syn PFFs for 24 hours. ** P < 0.01, *** P < 0.001, vs . 0 µg/mL group. (B) Western blot analysis of LRP1 and α-syn expression levels in PC12 cells. (C, D) Densitometric analysis of LRP1 (C) and α-syn (D) expression levels. (E) Immunofluorescence analysis of LRP1 (green, Alexa Fluor 488), α-syn (red, Alexa Fluor 594), and DAPI (blue) expression. The LRP1 and α-syn signal intensities were stronger in PFF group than in Con group. Scale bars: 40 μm. (F, G) Quantitative immunofluorescence intensity analysis of LRP1 (F) and α-syn (G). * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001, vs . Con group; # P < 0.05, ## P < 0.01, vs. monomer group. Data are expressed as mean ± SD ( n = 3). Con: Control; DAPI: 4′,6-diamidino-2-phenylindole; PFF: pre-formed fibril; LRP1: low-density lipoprotein receptor-related protein 1; α-syn: α-synuclein.

Article Snippet: α-Syn PFFs (SPR-322, StressMarq, Victoria, Canada) were sonicated with a handheld probe (VCX130, SONICS & MATERIALS, Newtown, CT, USA) as follows: amplitude 30% and time 15 seconds (pulse on 3 seconds, pulse off 6 seconds) (Volpicelli-Daley et al., 2014; Sun et al., 2022b).

Techniques: Expressing, Incubation, Western Blot, Immunofluorescence, Control

Journal: Neural Regeneration Research

Article Title: Low-density lipoprotein receptor–related protein 1 mediates α-synuclein transmission from the striatum to the substantia nigra in animal models of Parkinson’s disease

doi: 10.4103/NRR.NRR-D-23-01965

Figure Lengend Snippet: LRP1 knockdown rescues the dopaminergic damage induced by exogenous α-syn PFFs. (A, B) Western blot analysis (A) and densitometric analysis (B) of TH expression levels in the STR of mice treated with PFFs. (C, D) Western blot analysis (C) and densitometric analysis (D) of TH expression levels in the SN of mice treated with PFFs. (E) Immunohistochemistry staining for TH in the STR of mice treated with PFFs and LRP1 siRNA. The decrease in relative TH intensity in STR observed in the PFF group was rescued by LRP1 siRNA treatment. The images in the second row are enlarged images of the areas indicated by black boxes in the upper row. Scale bars: 200 μm, 40 μm (enlarged). (F) Quantitative immunohistochemistry density analysis of TH in the STR. (G) Immunohistochemistry analysis of TH in the SN of mice treated with PFFs. The decreased ratio of TH-positive neurons in the SN of the Scramble + PFF group (PFF group) was rescued by LRP1 siRNA treatment. The images in the second row are enlarged images of the areas indicated by black boxes in the upper row, and the white arrowheads indicate typical TH-positive neurons. Scale bars: 100 μm, 20 μm (enlarged). (H) Quantitation of the ratio of TH-positive neurons in the SN compared with the PBS group. Data are expressed as mean ± SD ( n = 3). * P < 0.05, ** P < 0.01, *** P < 0.001, vs. Scramble + PBS group (PBS group); # P < 0.05, ## P < 0.01, vs. scramble + PFF group (PFF group). LRP1: Low-density lipoprotein receptor-related protein 1; PBS: phosphate buffered solution; PFF: pre-formed fibril; siRNA: small interfering RNA; SN: substantia nigra; STR: striatum; TH: tyrosine hydroxylase; α-syn: α-synuclein.

Article Snippet: α-Syn PFFs (SPR-322, StressMarq, Victoria, Canada) were sonicated with a handheld probe (VCX130, SONICS & MATERIALS, Newtown, CT, USA) as follows: amplitude 30% and time 15 seconds (pulse on 3 seconds, pulse off 6 seconds) (Volpicelli-Daley et al., 2014; Sun et al., 2022b).

Techniques: Knockdown, Western Blot, Expressing, Immunohistochemistry, Staining, Quantitation Assay, Small Interfering RNA

Journal: Neural Regeneration Research

Article Title: Low-density lipoprotein receptor–related protein 1 mediates α-synuclein transmission from the striatum to the substantia nigra in animal models of Parkinson’s disease

doi: 10.4103/NRR.NRR-D-23-01965

Figure Lengend Snippet: LRP1 suppression reduces the transmission of exogenous α-syn in vivo . (A) Immunofluorescence staining for LRP1 (green, Alexa Fluor 488), α-syn (red, Alexa Fluor 594), and DAPI (blue) in the mouse STR after stereotactic injection with α-syn PFFs for 6 weeks with or without LRP1 knockdown. The increase in the relative fluorescence intensity of LRP1 and α-syn in the STR of PFFs-treated mice was rescued by LRP1 siRNA treatment. Scale bars: 100 μm. (B, C) Quantitative immunofluorescence intensity of LRP1 (B) and α-syn (C) in mouse STR. (D) Immunofluorescence staining for LRP1 (green, Alexa Fluor 488), α-syn (red, Alexa Fluor 594), and DAPI (blue) in the SN of mice after stereotactic injection with α-syn PFFs for 6 weeks with or without LRP1 knockdown. The increase in the relative fluorescence intensity of LRP1 and α-syn in the SN of mice treated with PFFs was rescued by LRP1 siRNA treatment. The white arrowheads indicate typical cells exhibiting α-syn and LRP1 expression. Scale bars: 100 μm. (E, F) Quantitative immunofluorescence intensity of LRP1 (E) and α-syn (F) in the mouse SN. (G) Western blot analysis of LRP1 and α-syn expression levels in the mouse STR. (H, I) Densitometric analysis of LRP1 (H) and α-syn (I) expression levels in the mouse STR. (J) Western blot analysis of LRP1 and α-syn expression levels in the mouse SN. (K, L) Densitometric analysis of LRP1 (K) and α-syn (L) expression levels in the mouse SN. Data are expressed as mean ± SD ( n = 3). * P < 0.05, ** P < 0.01, vs. Scramble + PBS group (PBS group); # P < 0.05, ## P < 0.01, vs . Scramble + PFF group (PFF group). DAPI: 4′,6-Diamidino-2-phenylindole; LRP1: low-density lipoprotein receptor-related protein 1; PBS: phosphate buffered solution; PFF: pre-formed fibril; siRNA: small interfering RNA; SN: substantia nigra; STR: striatum; α-syn: α-synuclein.

Article Snippet: α-Syn PFFs (SPR-322, StressMarq, Victoria, Canada) were sonicated with a handheld probe (VCX130, SONICS & MATERIALS, Newtown, CT, USA) as follows: amplitude 30% and time 15 seconds (pulse on 3 seconds, pulse off 6 seconds) (Volpicelli-Daley et al., 2014; Sun et al., 2022b).

Techniques: Transmission Assay, In Vivo, Immunofluorescence, Staining, Injection, Knockdown, Fluorescence, Expressing, Western Blot, Small Interfering RNA

Journal: Neural Regeneration Research

Article Title: Low-density lipoprotein receptor–related protein 1 mediates α-synuclein transmission from the striatum to the substantia nigra in animal models of Parkinson’s disease

doi: 10.4103/NRR.NRR-D-23-01965

Figure Lengend Snippet: LRP1 mediates the uptake of α-syn PFFs by PC12 cells. (A) Western blot analysis of LRP1 and α-syn expression levels in PC12 cells with or without LRP1 knockdown (10 nM siRNA) after incubation with 10 µg/mL α-syn PFFs for 24 hours. (B, C) Densitometric analysis of LRP1 (B) and α-syn (C) expression. (D) Immunofluorescence staining for LRP1 (green, Alexa Fluor 488), α-syn (red, Alexa Fluor 594), and DAPI (blue). The increase in the relative fluorescence intensity levels of LRP1 and α-syn in the PFF group was rescued by LRP1 siRNA treatment. Scale bars: 40 μm. (E, F) Quantitative immunofluorescence intensity analysis of LRP1 (E) and α-syn (F). Data are expressed as mean ± SD ( n = 3). ** P < 0.01, *** P < 0.001, **** P < 0.0001, vs . Con group; # P < 0.05, ## P < 0.01, #### P < 0.0001, vs . PFF/– group. Con: Control; DAPI: 4′, 6-diamidino-2-phenylindole; PFF: pre-formed fibril; LRP1: low-density lipoprotein receptor-related protein 1; siRNA: small interfering RNA; α-syn: α-synuclein.

Article Snippet: α-Syn PFFs (SPR-322, StressMarq, Victoria, Canada) were sonicated with a handheld probe (VCX130, SONICS & MATERIALS, Newtown, CT, USA) as follows: amplitude 30% and time 15 seconds (pulse on 3 seconds, pulse off 6 seconds) (Volpicelli-Daley et al., 2014; Sun et al., 2022b).

Techniques: Western Blot, Expressing, Knockdown, Incubation, Immunofluorescence, Staining, Fluorescence, Control, Small Interfering RNA

Journal: Neural Regeneration Research

Article Title: Low-density lipoprotein receptor–related protein 1 mediates α-synuclein transmission from the striatum to the substantia nigra in animal models of Parkinson’s disease

doi: 10.4103/NRR.NRR-D-23-01965

Figure Lengend Snippet: Lysine residues in the α-syn N-terminus are vital for LRP1-mediated α-Syn internalization. (A) Heatmap of amino acids in different α-syn domains. (B) Western blot analysis of LRP1 and α-Syn levels in PC12 cells after addition of α-syn PFFs (10 µg/mL) with or without capping of lysine residues for 24 hours. (C, D) Densitometric analysis of LRP1 (C) and α-syn (D) expression levels. (E) Immunofluorescence staining for LRP1 (green, Alexa Fluor 488), α-Syn (red, Alexa Fluor 594), and DAPI (blue). The increase in the relative fluorescence intensity of LRP1 and α-syn in the PFF group was rescued by lysine capping of α-syn. Scale bars: 40 μm. (F, G) Quantitative immunofluorescence intensity analysis of LRP1 (F) and α-syn (G). Data are expressed as mean ± SD ( n = 3). * P < 0.05, ** P < 0.01, **** P < 0.0001, vs. Con group; # P < 0.05, ## P < 0.01, vs . PFF group. Con: Control; DAPI: 4′,6-diamidino-2-phenylindole; LRP1: low-density lipoprotein receptor-related protein 1; NHS: sulfo-NHS acetate; PFF: pre-formed fibril; α-syn: α-synuclein.

Article Snippet: α-Syn PFFs (SPR-322, StressMarq, Victoria, Canada) were sonicated with a handheld probe (VCX130, SONICS & MATERIALS, Newtown, CT, USA) as follows: amplitude 30% and time 15 seconds (pulse on 3 seconds, pulse off 6 seconds) (Volpicelli-Daley et al., 2014; Sun et al., 2022b).

Techniques: Western Blot, Expressing, Immunofluorescence, Staining, Fluorescence, Control

Journal: Alzheimer's & Dementia

Article Title: Single‐cell analysis reveals neuroprotective histone deacetylase inhibitor pathways

doi: 10.1002/alz.71108

Figure Lengend Snippet: Integrative multi‐cell type analysis workflow identifies DISC1 as a convergent target of TSA in AD. Schematic representation of the multi‐pronged analytical framework used to identify and validate TSA as a therapeutic candidate for AD. The workflow began with cell‐type‐specific drug repurposing analysis of scRNA‐seq data from Grubman et al., ¹³ Mathys et al., ¹⁴ and Green et al. ¹⁵ datasets, resulting in the identification of TSA as a promising compound. We strategically investigated TSA's effects through two parallel cell type‐specific pathways: neurons and microglia. These cell types were specifically selected based on their known vulnerability in AD pathology and significant drug scores in our initial ASGARD analysis. For neurons, we applied DEGAS analysis to identify AD‐associated neuronal subpopulations, followed by differential expression analysis of TSA‐treated neurons in mice. Concurrently, we examined microglia, which showed high TSA drug scores in doublet interactions, and conducted differential expression analysis across microglial subtypes. Both analytical branches converged on DISC1 as a key upregulated gene, which was subsequently validated in human iPSC‐derived neuronal models through both phenotypic assays and transcriptomic analysis. This cell type‐specific approach enabled the identification of DISC1 as a potential mechanistic target underlying TSA's neuroprotective effect in AD. Created in BioRender. Peyton, M. (2025) https://biorender.com/73irecf . AD, Alzheimer's disease; ASGARD, A Single Cell Guided Pipeline to Aid Repurposing of Drugs; DEGAS, Diagnostic Evidence Gauge of Single cells; DISC1, Disrupted‐In‐Schizophrenia 1; iPSC, induced pluripotent stem cell; scRNA‐seq, single‐cell RNA sequencing; TSA, trichostatin‐A.

Article Snippet: For experimental treatments, neurons were cultured until in vitro day (DIV) 4, at which point they were treated with various concentrations of TSA (TSA, Sigma–Aldrich, cat. #: T1952) and Aβ oligomers (StressMarq, cat. #: SPR‐488).

Techniques: Quantitative Proteomics, Derivative Assay, Diagnostic Assay, RNA Sequencing

Journal: Alzheimer's & Dementia

Article Title: Single‐cell analysis reveals neuroprotective histone deacetylase inhibitor pathways

doi: 10.1002/alz.71108

Figure Lengend Snippet: Single‐cell analysis identifies TSA as top drug repurposing candidate across cortical brain regions. (A) UMAP projections of all cells from six control and six AD samples in the Grubman et al. ¹³ entorhinal cortex dataset, with clusters representing cell‐type‐specific groupings. (B) Pathway enrichment analysis highlighting key signaling pathways significantly enriched within each cell type cluster in the Grubman dataset, with significance represented as ‐log10(FDR). (C) Drug Score analysis for AD samples in the Grubman dataset, displaying compounds with FDR < 0.1 and Drug Score ranking within the 90th percentile. TSA (trichostatin‐A) emerges among the top‐ranked candidates. (D) UMAP visualizations of all cells from 24 control and 24 AD samples in the Mathys et al. ¹⁴ prefrontal cortex dataset, with distinct clusters representing cell types. (E) Pathway enrichment analysis for the Mathys dataset showing key signaling pathways significantly enriched within each cell type cluster, with significance represented as ‐log10(FDR). (F) Drug Score analysis for AD samples in the Mathys dataset, displaying compounds with FDR < 0.1 and Drug Score values within the 90th percentile. (G) UMAP projections from the Green et al. ¹⁵ aged prefrontal cortex dataset showing cell‐type‐specific clustering across AD and control samples. (H) Pathway enrichment analysis for the Green dataset, highlighting significantly enriched signaling pathways across cell types, with significance represented as ‐log10(FDR). (I) Drug Score analysis for the Green dataset showing top‐ranked therapeutic candidates with FDR < 0.1 and Drug Scores within the 90th percentile. Cell types: Ast, astrocytes; CUX2+, CUX2‐positive excitatory neurons; CUX2‐, CUX2‐negative excitatory neurons; Dou, doublets; End, endothelial cells; Ex, excitatory neurons; In, inhibitory neurons; Inh, inhibitory neurons; Mic, microglia; Neu, neurons; Oli, oligodendrocytes; Opc, oligodendrocyte progenitor cells; Per, pericytes; unID, unidentified cells. AD, Alzheimer's disease; FDR, false discovery rate; TSA, trichostatin‐A; UMAP, Uniform Manifold Approximation and Projection.

Article Snippet: For experimental treatments, neurons were cultured until in vitro day (DIV) 4, at which point they were treated with various concentrations of TSA (TSA, Sigma–Aldrich, cat. #: T1952) and Aβ oligomers (StressMarq, cat. #: SPR‐488).

Techniques: Single-cell Analysis, Control, Protein-Protein interactions

Journal: Alzheimer's & Dementia

Article Title: Single‐cell analysis reveals neuroprotective histone deacetylase inhibitor pathways

doi: 10.1002/alz.71108

Figure Lengend Snippet: Doublet cell analysis reveals cellular interaction patterns and drug targeting opportunities in AD. (A) UMAP projections of all cells from six control and six AD samples in the Grubman et al. ¹³ dataset, showing cell‐type‐specific clusters with doublets re‐annotated into their most likely two contributing cell types (e.g., ast‐mic for astrocyte–microglia doublets). (B) Bar chart displaying the counts of identified cell types, including doublets without splitting into their component cell types. (C) Pie chart illustrating the distribution of identified doublet cell types, providing an overview of the most common cellular interactions observed in the dataset. (D) Pathway enrichment analysis for re‐annotated cell type clusters, highlighting key signaling pathways with significant enrichment, represented as ‐log10(FDR). (E) Drug Score analysis for AD samples, highlighting compounds with FDR < 0.1 and Drug Scores within the 90th percentile. TSA shows particularly strong enrichment in doublet populations involving microglia. Cell types: Ast, astrocytes; Dou, doublets; End, endothelial cells; Mic, microglia; Neu, neurons; Oli, oligodendrocytes; Opc, oligodendrocyte progenitor cells; unID, unidentified cells. AD, Alzheimer's disease; FDR, false discovery rate; UMAP, Uniform Manifold Approximation and Projection.

Article Snippet: For experimental treatments, neurons were cultured until in vitro day (DIV) 4, at which point they were treated with various concentrations of TSA (TSA, Sigma–Aldrich, cat. #: T1952) and Aβ oligomers (StressMarq, cat. #: SPR‐488).

Techniques: Cell Analysis, Control, Protein-Protein interactions

Journal: Alzheimer's & Dementia

Article Title: Single‐cell analysis reveals neuroprotective histone deacetylase inhibitor pathways

doi: 10.1002/alz.71108

Figure Lengend Snippet: TSA modulates synaptic and developmental gene programs and prevents Aβ‐induced neurotoxicity in human iPSC‐derived cortical neurons. (A) Volcano plot of DEGs in TSA‐treated mouse hippocampal neurons versus control. Blue points represent significantly downregulated genes, while red points represent significantly upregulated genes (adjusted p ‐value < 0.05). (B) GO Biological Process enrichment analysis for genes with positive log2 fold change (upregulated by TSA treatment). (C) GO Biological Process enrichment analysis for genes with negative log2 fold change (downregulated by TSA treatment). (D) Venn diagram showing overlapping upregulated genes across three independent analyses: TSA‐treated mouse hippocampal neurons (red, 5015 unique genes), microglial subtypes from the Lee et al. human dataset (blue, 419 unique genes), and AD‐associated neurons identified via DEGAS cell prioritization analysis (green, 142 unique genes). The diagram reveals 104 genes shared between the TSA and Lee datasets, 54 genes shared between the TSA and DEGAS, 4 genes shared between Lee and DEGAS, and critically, 1 gene (DISC1) upregulated across all three experimental contexts, identifying it as a convergent therapeutic target. (E) MTS cell viability assay results in human iPSC‐derived cortical neurons. Left panel: Dose‐response curve showing Aβ oligomer‐induced toxicity at concentrations of 0.2, 1, and 5 µM compared to control. Right panel: TSA neuroprotection against 5 µM Aβ oligomers, with neurons pre‐treated with varying TSA concentrations (0.066, 0.2, 0.33) showing dose‐dependent rescue of cell viability. Statistical significance: ns (not significant), ** p < 0.01, *** p < 0.001, **** p < 0.0001. (F) Quantification of synaptic cluster density (number of clusters per 20 µm dendrite) across treatment conditions. NT neurons show baseline synaptic density (gray), 5 µM) cause significant synaptic loss (red), and co‐treatment with 0.2 µM TSA (Aβo + TSA, green) significantly rescues synaptic density, demonstrating TSA's protective effect on synaptic integrity. Each dot represents an individual measurement. Statistical significance: ns (not significant), **** p < 0.0001. (G) Representative confocal immunofluorescence images of synapses in human iPSC‐derived cortical neurons. Neurons were immunostained for the postsynaptic marker PSD95 (red, left column) and presynaptic marker Syn1 (green, middle column), with colocalization (yellow, right column) indicating functional synapses. Rows show: NT controls (top), 5 µM Aβo treatment (middle), and combined treatment with Aβo plus 0.2 µM TSA (Aβo+TSA, bottom). TSA treatment preserves synaptic density and colocalization despite Aβ exposure. Scale bar = 2 µm. Aβ, β‐amyloid; Aβo, Aβ oligomers; AD, Alzheimer's disease; DEG, differentially expressed genes; DEGAS, Diagnostic Evidence Gauge of Single cells; GO, gene ontology; iPSC, induced pluripotent stem cell; NT, non‐treated; TSA, trichostatin‐A.

Article Snippet: For experimental treatments, neurons were cultured until in vitro day (DIV) 4, at which point they were treated with various concentrations of TSA (TSA, Sigma–Aldrich, cat. #: T1952) and Aβ oligomers (StressMarq, cat. #: SPR‐488).

Techniques: Derivative Assay, Control, Viability Assay, Immunofluorescence, Marker, Functional Assay, Diagnostic Assay

Journal: Alzheimer's & Dementia

Article Title: Single‐cell analysis reveals neuroprotective histone deacetylase inhibitor pathways

doi: 10.1002/alz.71108

Figure Lengend Snippet: Transcriptomic analysis of TSA effects on iPSC‐derived cortical neurons reveals distinct gene expression patterns . (A) Volcano plot displaying DEGs between control and TSA‐treated human iPSC‐derived cortical neurons. Significantly upregulated genes are shown in red and downregulated genes in blue (adjusted p ‐value < 0.05, |log 2 FC| > 0.58). (B) Box plots showing DISC1 expression levels (normalized log2CPM) across four treatment conditions: Control, Amyloid_beta (Aβ alone), TSA (TSA alone), and Combined (TSA + Aβ). Statistical comparisons are indicated with brackets and significance levels. (C) GO Biological Process enrichment analysis for genes upregulated by TSA treatment. Dot size represents gene count, and color indicates ‐log 10 (FDR). (D) GO Biological Process enrichment analysis for genes downregulated by TSA treatment. (E) GO Molecular Function enrichment for genes upregulated by TSA treatment. (F) GO Molecular Function enrichment for genes downregulated by TSA treatment. (G) Heatmap showing expression patterns of top differentially expressed genes across all samples. Samples are grouped by treatment condition (Control, Amyloid_beta, TSA, Combined) with color‐coded bars at the top. Gene expression is displayed as normalized z ‐scores, with red indicating high expression and blue indicating low expression. Aβ, β‐amyloid; DEG, differentially expressed genes; DISC1, Disrupted‐In‐Schizophrenia 1; FDR, false discovery rate; GO, gene ontology; iPSC, induced pluripotent stem cell; TSA, trichostatin‐A.

Article Snippet: For experimental treatments, neurons were cultured until in vitro day (DIV) 4, at which point they were treated with various concentrations of TSA (TSA, Sigma–Aldrich, cat. #: T1952) and Aβ oligomers (StressMarq, cat. #: SPR‐488).

Techniques: Derivative Assay, Gene Expression, Control, Expressing

Journal: Alzheimer's & Dementia

Article Title: Single‐cell analysis reveals neuroprotective histone deacetylase inhibitor pathways

doi: 10.1002/alz.71108

Figure Lengend Snippet: Differential gene expression analysis of TSA and amyloid‐beta treatment in neural cells. (A) Volcano plot showing the main effect of Aβ treatment on gene expression (Amyloid‐beta Main Effect). Significantly downregulated genes are shown in blue and upregulated genes in red (adjusted p ‐value < 0.05, |log 2 FC| > 0.58). (B) Volcano plot displaying the main effect of TSA treatment on gene expression (TSA Main Effect). Significantly downregulated genes are shown in blue and upregulated genes in red. (C) Volcano plot illustrating the interaction effect between TSA and Aβ treatments (TSA:Amyloid‐beta Interaction Effect). Significantly downregulated genes are shown in blue and upregulated genes in red. (D) Heatmap displaying expression patterns of top differentially expressed genes across experimental conditions, clustered by effect type. Samples are organized by treatment condition: Control, AB (Aβ), TSA, and TSA+AB (Combined). Left sidebar color bars indicate Condition (Control, Amyloid_beta, TSA, Combined). Right sidebar color bars indicate Direction (Up, Down) and Effect (TSA, Amyloid‐beta, Interaction). Expression values are shown as normalized z ‐scores with yellow indicating high expression and blue indicating low expression. Aβ, β‐amyloid; TSA, trichostatin‐A.

Article Snippet: For experimental treatments, neurons were cultured until in vitro day (DIV) 4, at which point they were treated with various concentrations of TSA (TSA, Sigma–Aldrich, cat. #: T1952) and Aβ oligomers (StressMarq, cat. #: SPR‐488).

Techniques: Gene Expression, Expressing, Control