Journal: EMBO Molecular Medicine

Article Title: Spatial transcriptomics elucidates localized immune responses in atherosclerotic coronary artery

doi: 10.1038/s44321-025-00280-w

Figure Lengend Snippet: ( A ) Representative haematoxylin and eosin (H&E) stained sections showing arterial lesions of varying severity (mild, moderate and severe). Specific regions are highlighted at a higher magnification to reveal morphological differences across lesion severity, indicating progressive changes from near normal to severe. ( B ) Workflow for spatial transcriptomics using GeoMx® DSP: slide preparation with morphology markers and ~18,000 oligo-conjugated RNA probes; selection of ROIs in each sample analysed; cleavage with UV light of barcodes from RNA probes; collection and release of collected barcodes onto a 96-well plate for all selected ROIs; generation of a cDNA library for next generation sequencing and upload of resulting sequencing data onto the GeoMx® DSP. ( C ) Fluorescent imaging of arterial lesions with varying severities, reflecting those shown at higher magnification in ( A ). Fluorescent imaging is a prerequisite for choosing regions of interest (ROIs) for downstream profiling by GeoMx. Samples were stained with SYTO13 (nuclear dye, blue), CD45 (pan-leucocyte marker, yellow) and CD4 (T cell subset marker, red). Representative ROIs chosen for downstream spatial profiling are indicated by white circles. .

Article Snippet: Specific regions are highlighted at a higher magnification to reveal morphological differences across lesion severity, indicating progressive changes from near normal to severe. ( B ) Workflow for spatial transcriptomics using GeoMx® DSP: slide preparation with morphology markers and ~18,000 oligo-conjugated RNA probes; selection of ROIs in each sample analysed; cleavage with UV light of barcodes from RNA probes; collection and release of collected barcodes onto a 96-well plate for all selected ROIs; generation of a cDNA library for next generation sequencing and upload of resulting sequencing data onto the GeoMx® DSP. ( C ) Fluorescent imaging of arterial lesions with varying severities, reflecting those shown at higher magnification in ( A ).

Techniques: Staining, Selection, cDNA Library Assay, Next-Generation Sequencing, Sequencing, Imaging, Marker

Journal: Nature Communications

Article Title: Targeting SPAK suppresses progression and averts an immune exhaustive microenvironment in hepatocellular carcinoma

doi: 10.1038/s41467-025-68156-8

Figure Lengend Snippet: a Representative tissue region maps and expression analysis of SPAK levels from a spatial transcriptome dataset of ICI responders and non-responders (Mendeley Data: skrx2fz79n). b Representative abdominal MRI images, representative IHC staining and quantitative IHC analysis of SPAK levels performed on human HCC tissue obtained before and after treatment of ICI responders ( n = 7 patients) and non-responders ( n = 12 patients) (scale bars, 100 μm). c A schematic representation of the treatment strategy in the DEN/CCl4-induced HCC model. d , e Gross images of livers (scale bars, 5 mm), representative H&E staining (scale bars, 1000 μm), and tumor burden ( n = 5 mice) from the indicated DEN/CCl4-induced HCC model. f A schematic representation of the treatment strategy in the AKT/NRasV12 -induced HCC model. g , h Gross images of livers (scale bars, 5 mm), representative H&E staining (scale bars, 1000 μm), and tumor burden ( n = 5 mice) from the indicated AKT/NRasV12-induced HCC model. i A schematic representation of the treatment strategy in the Hepa1-6-induced HCC model. j , k Gross images of livers (scale bars, 5 mm), representative H&E staining (scale bars, 200 μm), and tumor burden ( n = 6 mice) from the indicated Hepa1-6-induced HCC model. l , m Total flux curve and bioluminescence images of mice from the indicated Hepa1-6-induced HCC model for the indicated days ( n = 6 mice); a , b , e , h , k , m P values were calculated using an unpaired t test (two-tailed). The box plots show data distribution with the overlaid box plot indicating the median, first (Q1) and third (Q3) quartiles, and the whiskers extending to the 1.5× interquartile range (IQR). Source data are provided as a file.

Article Snippet: Fig. 8 Combined targeting SPAK and PD-1 showed enhanced efficacy in HCC. a Representative tissue region maps and expression analysis of SPAK levels from a spatial transcriptome dataset of ICI responders and non-responders (Mendeley Data: skrx2fz79n). b Representative abdominal MRI images, representative IHC staining and quantitative IHC analysis of SPAK levels performed on human HCC tissue obtained before and after treatment of ICI responders ( n = 7 patients) and non-responders ( n = 12 patients) (scale bars, 100 μm). c A schematic representation of the treatment strategy in the DEN/CCl4-induced HCC model. d , e Gross images of livers (scale bars, 5 mm), representative H&E staining (scale bars, 1000 μm), and tumor burden ( n = 5 mice) from the indicated DEN/CCl4-induced HCC model. f A schematic representation of the treatment strategy in the AKT/NRasV12 -induced HCC model. g , h Gross images of livers (scale bars, 5 mm), representative H&E staining (scale bars, 1000 μm), and tumor burden ( n = 5 mice) from the indicated AKT/NRasV12-induced HCC model. i A schematic representation of the treatment strategy in the Hepa1-6-induced HCC model. j , k Gross images of livers (scale bars, 5 mm), representative H&E staining (scale bars, 200 μm), and tumor burden ( n = 6 mice) from the indicated Hepa1-6-induced HCC model. l , m Total flux curve and bioluminescence images of mice from the indicated Hepa1-6-induced HCC model for the indicated days ( n = 6 mice); a , b , e , h , k , m P values were calculated using an unpaired t test (two-tailed).

Techniques: Expressing, Immunohistochemistry, Staining, Two Tailed Test

Journal: Advanced Science

Article Title: NDST3‐Induced Epigenetic Reprogramming Reverses Neurodegeneration in Parkinson's Disease

doi: 10.1002/advs.202507323

Figure Lengend Snippet: Identification of regenerating factor as a regulator of therapeutic genes for Parkinson's disease therapy. A) Conceptual diagram outlining the basis of an epigenetic regulator. B) Comparative gene expression heatmap of substantia nigra (SN) in wild type control versus 6‐OHDA‐induced Parkinson's disease (PD) mouse model. C) Heatmap showing gene expression profiles in the caudate and putamen regions of healthy individuals (HI) and a cohort of human PD patients. BG: Basal Ganglia. D) Immunofluorescence images showing TUJ1‐ and MAP2‐positive cells under each condition. Scale bar = 50 µm. E) Immunochemistry and Sholl analysis of TH‐labeled neurons. Left panel: morphology of individual neurons. Right panel: Sholl analysis showing the number of neurite intersections as a function of distance from the soma. Scale bar = 100 µm. The data are presented as mean ± SEM ( n = 5 – 6 cells per group). F) Representative traces of action potentials evoked by depolarizing current injections under each condition (sham, 6‐OHDA, 6‐OHDA+NDST3). G) Dot plot showing the top 14 GO Biological Process terms from enrichment analyses: 6‐OHDA versus Sham (left side) and 6‐OHDA+NDST3 versus 6‐OHDA (right side). H) Pearson correlation matrix of transcriptomic among samples.

Article Snippet: Slices were incubated with primary antibodies targeting dopaminergic neuron markers TH (Merck Millipore, AB152, Lot# 4127053; Merck Millipore, MAB318, Lot#3990619), GIRK2 (Abcam, ab259909, Lot# GR3401320‐4), NDST3 (Novus Biologicals, NBP2‐19501, Lot# 40723), DAT (Merck Millipore, MAB369) and histone modification marker H3K27ac (Abcam, AB4729, Lot# 1059037‐6).

Techniques: Gene Expression, Control, Immunofluorescence, Labeling

Journal: Advanced Science

Article Title: NDST3‐Induced Epigenetic Reprogramming Reverses Neurodegeneration in Parkinson's Disease

doi: 10.1002/advs.202507323

Figure Lengend Snippet: Therapeutic efficacy of NDST3 and retrograde tracing with CTB in mice. A) Schematic diagram of in vivo experimental design involving CTB injection in the PD mouse model. B) Representative immunofluorescence images of CTB, TH, and NDST3 expression in the SN of Sham, 6‐OHDA‐induced PD mice, and NDST3‐treated PD mice. Scale bar = 50 µm and 10 µm (Magnified image). C) Quantification of CTB‐, TH‐, and NDST3‐positive cells shown in Figure . Data are presented as mean ± SEM ( n = 6 independent animals per group). One‐way ANOVA with Tukey's multiple comparisons test. ** p < 0.01, *** p < 0.001, **** p < 0.0001, and ns = not significant. D) Immunofluorescence images showing GIRK2‐ and TH‐positive cells in the Sham, 6‐OHDA‐induced PD mice, and NDST3‐treated PD mice. Scale bar = 50 µm and 10 µm (Magnified image). E) 3D Z‐stack analysis (IMARIS) of TH‐positive neurons obtained via confocal microscopy. F) DAB‐DAT staining in the SN.

Article Snippet: Slices were incubated with primary antibodies targeting dopaminergic neuron markers TH (Merck Millipore, AB152, Lot# 4127053; Merck Millipore, MAB318, Lot#3990619), GIRK2 (Abcam, ab259909, Lot# GR3401320‐4), NDST3 (Novus Biologicals, NBP2‐19501, Lot# 40723), DAT (Merck Millipore, MAB369) and histone modification marker H3K27ac (Abcam, AB4729, Lot# 1059037‐6).

Techniques: Drug discovery, Retrograde Tracing, In Vivo, Injection, Immunofluorescence, Expressing, Confocal Microscopy, Staining

Journal: Advanced Science

Article Title: NDST3‐Induced Epigenetic Reprogramming Reverses Neurodegeneration in Parkinson's Disease

doi: 10.1002/advs.202507323

Figure Lengend Snippet: Efficacy and electrophysiological properties of NDST3 in chemical‐induced PD model. A) Representative traces of spontaneous firing currents recorded from DA neurons of the SNpc in brain slices from each group. B) Cumulative fractions curves showing shortened inter‐event intervals, indicating a higher frequency of spontaneous firing in the 6‐OHDA + NDST3 group compared to the 6‐OHDA group. The inner bar graph showed mean inter‐event intervals in the ipsilateral of SNpc of each group. Data are presented as mean ± SEM ( n = 6 – 8 independent animals per group). One‐way ANOVA with Tukey's multiple comparisons test. *** p < 0.001. C) Quantification of DA neuronal firing rates in the ipsilateral SNpc of each group. The data are presented as mean ± SEM ( n = 6–8 independent animals per group). One‐way ANOVA with Tukey's multiple comparisons test. * p < 0.05, and ** p < 0.01. D) Representative in vivo recording traces from the SNpc of live animals in each condition. E) Instantaneous firing frequencies during the recorded period. ( n = 4–6 independent animals per group; repeated measures) Two‐way ANOVA with Tukey's multiple comparisons test, * p < 0.05. F) Comparison of action potential waveforms among DA neurons across conditions. G) Representative image of DAB‐TH staining in ST and SN. Scale bar = 1 mm. H) Immunofluorescence images showing GIRK2‐ and TH‐positive cells in the Sham, MPTP‐induced PD mice, NDST3‐treated PD mice, and NDST3 only‐treated mice. Scale bar = 50 µm and 10 µm (Magnified image). I) Error count during the challenging beam traversal test for each experimental condition. The data are presented as mean ± SEM. ( n = 7 – 8 independent animals per group) Two‐way ANOVA with Tukey's multiple comparisons test. **** p < 0.0001. J) Errors per step during the challenging beam traversal test across conditions. The data are presented as mean ± SEM ( n = 7 – 8 independent animal per group). One‐way ANOVA with Tukey's multiple comparisons test. **** p < 0.0001. K) Fall latency in the wire‐hanging test. The data are presented as mean ± SEM ( n = 7–8 independent animals per group). One‐way ANOVA with Tukey's multiple comparisons test. *** p < 0.001 and **** p < 0.0001. L) Time to orient downward (T‐turn) and M) time to descend to the base (T‐total). The data are presented as mean ± SEM ( n = 7–8 independent animals per group). One‐way ANOVA with Tukey's multiple comparisons test. * p < 0.05, *** p < 0.001 and **** p < 0.0001.

Article Snippet: Slices were incubated with primary antibodies targeting dopaminergic neuron markers TH (Merck Millipore, AB152, Lot# 4127053; Merck Millipore, MAB318, Lot#3990619), GIRK2 (Abcam, ab259909, Lot# GR3401320‐4), NDST3 (Novus Biologicals, NBP2‐19501, Lot# 40723), DAT (Merck Millipore, MAB369) and histone modification marker H3K27ac (Abcam, AB4729, Lot# 1059037‐6).

Techniques: In Vivo, Comparison, Staining, Immunofluorescence

Journal: Advanced Science

Article Title: NDST3‐Induced Epigenetic Reprogramming Reverses Neurodegeneration in Parkinson's Disease

doi: 10.1002/advs.202507323

Figure Lengend Snippet: Molecular mechanisms of NDST3 in the PD model. A) One‐way hierarchical clustering heatmap based on Z‐score of normalized expression value for 5629 genes selected with fold change ≥ 2 and raw p ‐value < 0.05. B) Principal component analysis (PCA) analysis of RNA‐seq data to visualize sample‐to‐sample variation. C) Volcano plot showing differentially expressed genes between 6‐OHDA and Sham group; Down‐regulated genes marked in blue. D) Volcano plot showing differentially expressed genes between 6‐OHDA+NDST3 and 6‐OHDA; Up‐regulated genes marked in red. E) Dot plot of top 14 GO cellular component terms from GO enrichment analyses: 6‐OHDA+NDST3 versus 6‐OHDA. Heatmap showing gene expression patterns in F) pre‐synaptic neurons, G) post‐synaptic neurons, and H) glia compartments. I) UMAP visualizing cluster identity. J) UMAP representation comparing cellular composition in 6‐OHDA and 6‐OHDA+NDST3. K) Branched trajectory analysis illustrating cell state transitions in a 2D state‐space, where each dot represents a single cell, color‐coded by group identity.

Article Snippet: Slices were incubated with primary antibodies targeting dopaminergic neuron markers TH (Merck Millipore, AB152, Lot# 4127053; Merck Millipore, MAB318, Lot#3990619), GIRK2 (Abcam, ab259909, Lot# GR3401320‐4), NDST3 (Novus Biologicals, NBP2‐19501, Lot# 40723), DAT (Merck Millipore, MAB369) and histone modification marker H3K27ac (Abcam, AB4729, Lot# 1059037‐6).

Techniques: Expressing, RNA Sequencing, Gene Expression, Single Cell

Journal: Advanced Science

Article Title: NDST3‐Induced Epigenetic Reprogramming Reverses Neurodegeneration in Parkinson's Disease

doi: 10.1002/advs.202507323

Figure Lengend Snippet: Comprehensive analysis of spatial transcriptomics and epigenetic modulation following NDST3 treatment in a PD model. A) Heatmap showing gene expression patterns in each cluster. ** p < 0.01, and **** p < 0.0001. B) Gene concept network plot displaying genes enriched in catabolic, metabolic, and wound healing GO categories. The top 30 most differentially expressed genes comparing 6‐OHDA versus Sham and 6‐OHDA+NDST3 versus 6‐OHDA. Node color intensity represents the log2 fold‐change of gene expression. C) Cell‐cell communication network plot illustrating interactions among three distinct cell clusters in 6‐OHDA‐induced PD model (left panel) and NDST3‐treated PD model (right panel), based on ligand–receptor pair probabilities using the CellChat database. Line thickness indicates proportionality to the number of interactions. D) Spatial localization of dopamine‐related markers. E) Spatial mapping of dopaminergic lineage markers identified via scRNA‐Seq. F) Heatmap visualization of CUT&RUN and ATAC‐Seq signal intensity ±2 kb around the TSS. G) Immunofluorescence images showing H3K27ac and TH‐positive cells in the Sham, 6‐OHDA‐induced PD mice, and NDST3‐treated PD mice. Scale bar = 50 µm. H) Venn diagram illustrating overlapping genes among DEGs from RNA‐Seq, scRNA‐Seq Cluster 9, CUT&RUN peak, and ATAC‐Seq peak. Average signal plot of I) CUT&RUN and J) ATAC‐seq signals at over‐enriched TSS regions of the Ncoa7 gene. K) Structure of NDST3‐NCOA7‐H3K27ac complex. Blue – NDST3, Green – NCOA7, and Red – H3K27ac. The yellow boundary represents the interaction region.

Article Snippet: Slices were incubated with primary antibodies targeting dopaminergic neuron markers TH (Merck Millipore, AB152, Lot# 4127053; Merck Millipore, MAB318, Lot#3990619), GIRK2 (Abcam, ab259909, Lot# GR3401320‐4), NDST3 (Novus Biologicals, NBP2‐19501, Lot# 40723), DAT (Merck Millipore, MAB369) and histone modification marker H3K27ac (Abcam, AB4729, Lot# 1059037‐6).

Techniques: Spatial Transcriptomics, Gene Expression, Immunofluorescence, RNA Sequencing

Journal: Nature Communications

Article Title: DNA origami scaffold for studying intrinsically disordered proteins of the nuclear pore complex

doi: 10.1038/s41467-018-03313-w

Figure Lengend Snippet: Attachment of NSP1 and NSP1-S to the DNA ring. Top: laser-scanned EtBr images of ( a ) 1% agarose gel on which DNA origami ring samples were electrophoresed. Middle: same gel scanned in Cy5 excitation/emission channels. Cy5-labeled DNA strands were added to FG-Nup attachments where indicated. Bottom: integrated Cy5 band intensity normalized to EtBr intensity. b Histogram of the number of attached Cy5-labeled oligomers for an 8-attachment ring. Inset shows an exemplary intensity trace of a single-particle recording of a DNA ring with 8 attachment sites incubated with the complementary Cy5-labeled oligonucleotide obtained using total internal reflection microscopy (TIRF) (Methods section and Supplementary Figure ). See Supplementary Figure for additional intensity traces. c – e Exemplary field-of-view negative staining TEM micrographs of DNA origami NCP-mimic ring without protein, with 32-NSP1, and 32-NSP1-S, respectively. See Supplementary Figure for exemplary particles. Scale bar = 50 nm

Article Snippet: Fig. 3 Spatial distribution of FG-Nup densities in DNA rings from cryo-EM and MD simulations. a Schematic representation of (top to bottom): empty ring, 32-NSP1, and 32-NSP1-S. b Corresponding average obtained from aligning and summing individual cryo-EM particles.

Techniques: Agarose Gel Electrophoresis, Labeling, Single Particle, Incubation, Microscopy, Negative Staining

Journal: Nature Communications

Article Title: DNA origami scaffold for studying intrinsically disordered proteins of the nuclear pore complex

doi: 10.1038/s41467-018-03313-w

Figure Lengend Snippet: Spatial distribution of FG-Nup densities in DNA rings from cryo-EM and MD simulations. a Schematic representation of (top to bottom): empty ring, 32-NSP1, and 32-NSP1-S. b Corresponding average obtained from aligning and summing individual cryo-EM particles. Number of averaged particles: Ring = 1663, NSP1 = 637, NSP1-S = 1051. See Supplementary Figure for exemplary particles. Scale bar = 50 nm. c , d Time-averaged mass densities of proteins inside the DNA ring obtained from coarse-grained MD simulations averaged in the z -direction, shown in top view ( c ) and side view ( d ). e Exemplary snapshot of MD simulations of 32-NSP1 (top) and 32-NSP1-S (bottom), showing that NSP1-S proteins extend further out than NSP1

Article Snippet: Fig. 3 Spatial distribution of FG-Nup densities in DNA rings from cryo-EM and MD simulations. a Schematic representation of (top to bottom): empty ring, 32-NSP1, and 32-NSP1-S. b Corresponding average obtained from aligning and summing individual cryo-EM particles.

Techniques: Cryo-EM Sample Prep

Journal: Nature Communications

Article Title: DNA origami scaffold for studying intrinsically disordered proteins of the nuclear pore complex

doi: 10.1038/s41467-018-03313-w

Figure Lengend Snippet: Ionic conductance of rings with FG-Nups docked on a solid-state nanopore. a Schematic representation of DNA ring that is docking onto a solid-state nanopore. b Exemplary current (nA) versus voltage (mV) traces for rings without proteins, 8-NSP1, 32-NSP1 and 32-NSP1-S and the bare nanopore. c Exemplary relative conductance ( G ring / G pore ) vs time (s) traces showing the change in conductance upon docking of the ring without protein (gray), 32-NSP1 (yellow), and 32-NSP1-S (blue). d Box plot representation of the relative conductance ( G ring / G pore ) for the empty ring, 8-NSP1 and 32-NSP1. e Same as ( d ), but for empty ring, 8-NSP1-S and 32-NSP1-S. f Same as ( d ), but for empty ring, 8-NSP1 and 8-NSP1-S. g Same as ( d ), but for empty ring, 32-NSP1 and 32-NSP1-S. Each of the panels d – g represents a different nanopore experiment where a series of rings are probed on one particular solid-state nanopore. In the box plot representation in d – g , the blue boxes denote the 25th and 75th percentiles and the red lines represent the median values with the associated wedges representing a 95% confidence interval for the medians (see methods and Supplementary Table ). h Side view ( rz plane) average density distribution for 32-NSP1 placed on a 20 nm-wide nanopore in a 20 nm thin SiN membrane (see Supplementary Figure for an exemplary simulation snapshot and Fig. S15 for density distributions of other variants). i Comparison of experimental reduced conductance values and simulation results (Supplementary Note and Supplementary Tables and )

Article Snippet: Fig. 3 Spatial distribution of FG-Nup densities in DNA rings from cryo-EM and MD simulations. a Schematic representation of (top to bottom): empty ring, 32-NSP1, and 32-NSP1-S. b Corresponding average obtained from aligning and summing individual cryo-EM particles.

Techniques: