Journal: Nature Communications

Article Title: Isotope-encoded spatial biology identifies plaque-age-dependent maturation and synaptic loss in an Alzheimer’s disease mouse model

doi: 10.1038/s41467-025-63328-y

Figure Lengend Snippet: A PULSE-CHASE iSILK paradigm. Experimental Design 1: PULSE period ( 15 N diet) between 6-10 months of age. Experimental Design 2: PULSE period between 6-10 months of age, CHASE period ( 14 N diet) between 10–18 months of age. Resulting Aβ1-42 MALDI MS isotopologue pattern that is right-shifted (Δm) due to increasing 15 N incorporation. B Representative images of plaque load from GeoMx whole slide scans, repeated on four independent whole-brain slices at 18-months and three at 10-months. C MALDI MSI single ion image of Aβ1-42 in cortex section. D Schematic overview of the correlative hyperspectral imaging and MALDI MSI experiment. 15 N enrichment (nitrogen index) was calculated as the AUC ratio of the 4th to 3rd peak in the Aβ1-42 isotopologue pattern. Higher values indicate greater 15 N incorporation. E Schematic overview of the correlative spatial transcriptomics (GeoMx) and MALDI MSI experiment. Stable 15 N enrichments (nitrogen index) corresponding to plaque age was calculated by extracting the FWHM of the Aβ1-42 peak, where a broader peak indicates increased 15 N incorporation and higher age. F Schematic overview of the validation experiment. Plaque morphology was evaluated by LCO hyperspectral imaging. IHC of selected proteins were correlated with plaque age, as evaluated by hyperspectral imaging. G Representative spectra from MALDI MSI showing the 14 N and 15 N-enriched Aβ1-42 m/z peak. H Aβ1-42 mass analysis comparing the plaque center (Cen) vs. the periphery (Peri) in 10-month-old mice ( p = 0.00017), ( I ) in 18-month-old mice ( p = 0.00000077), and ( J ) differences between cortex and hippocampus ( p = 0.022). H , I Linear Mixed Model accounting for across animals and repeated measures, point color indicates animal, 15 replicates over n = 3 m mice and 22 replicates over n = 4 m mice, respectively. J Two-sided Paired t-test, 22 replicates over n = 4 m mice, data presented as mean ± SEM. K Representative MALDI MSI image of 15 N and 14 N enriched Aβ1-42 distribution in plaques in 18-month-old mice. Parts of the figure created in BioRender. Szadziewska, A. ( https://BioRender.com/4qpojxz ) Image in ( E ) provided by Bruker Spatial Biology. Significance levels: *** P < 0.001, ** P < 0.01; * P < 0.05. Source data are provided as a Source Data file. FWHM full width at half maximum, RP reflector mode, LP linear mode.

Article Snippet: The spatial transcriptomics platform GeoMx® Digital Spatial Profiler was selected over other sequencing techniques due to its ability to target plaque-specific gene expression changes, offering a more spatially resolved technique for AD pathology-associated alterations compared to the more commonly used RNA sequencing methods .

Techniques: Pulse Chase, Imaging, Biomarker Discovery

Journal: bioRxiv

Article Title: Imp1 acts as a dosage- and stage-dependent temporal rheostat orchestrating radial glial fate transitions and cortical morphogenesis

doi: 10.1101/2025.11.18.688993

Figure Lengend Snippet: (A,D,G) Representative images of control, continuous Imp1 overexpression, and T1 Imp1 conditions showing TEMPO reporters, Cux1/Ctip2 immunostaining and overlays. Boxed regions: Ctip2+ TEMPO neurons (dashed) or double-positive Cux1+/Ctip2+ TEMPO cells (solid). (B,E,H) High magnification images of boxed regions highlight CFP-/RFP-labeled neurons in layers V-VI colocalizing with Ctip2 (outlined arrowheads) or double-positive for both markers (solid arrowheads). (C,F,I) Quantification of marker expression in CFP+ and RFP+ neurons residing in layers V-VI. Following continuous or T1 Imp1 overexpression, neurons in deep layer maintain appropriate deep-layer molecular identities (predominantly Ctip2+), demonstrating that laminar distribution reflects bona fide fate specification changes rather than mislocalization. (C) In control conditions, CFP+: Ctip2 (78.31% ± 13.82%), Cux1 (2.93% ± 2.11%), double-negative (18.76% ± 11.73%). RFP+: Ctip2 (50.35% ± 17.01%), Cux1 (1.85% ± 1.85%), double-negative (46.76% ± 17.20%), double-positive (1.04% ± 1.04%). (F) Following continuous Imp1 overexpression, CFP+: Ctip2+ (71.18% ± 3.06%), Cux1+ (7.38% ± 4.93%), double-negative (16.06% ± 1.93%), double-positive (5.38% ± 1.80%). RFP+: Ctip2+ (58.92% ± 7.18%), Cux1+ (5.84% ± 3.01%), double-negative (5.10% ± 3.12%), double-positive (30.14% ± 11.98%). (I) In T1 Imp1 overexpression, CFP+: Ctip2+ (47.26% ± 4.88%), Cux1+ (14.63% ± 3.76%), double-negative (36.41% ± 5.64%), double-positive (1.68% ± 0.57%). RFP+: Ctip2+ (47.38% ± 13.91%), Cux1+ (9.17% ± 4.68%), double-negative (26.86% ± 5.03%), double-positive (16.59% ± 10.02%). Dashed lines: upper (II-IV), lower cortical layers (V-VI) and subplate zone (SPZ). Scale bars: (A,D,G) 100 µm and (B,E,H) 20 µm. Data show mean±SEM. Statistics: two-tailed unpaired Welch’s t-test (*P < 0.05, **P < 0.01, *** P < 0.001).

Article Snippet: Spatial transcriptomics profiling TEMPO+ populations at multiple developmental stages would reveal the full spectrum of molecular changes and identify specific transcript targets whose stabilization drives the observed phenotypes.

Techniques: Control, Over Expression, Immunostaining, Labeling, Marker, Expressing, Two Tailed Test

Journal: Journal of Translational Medicine

Article Title: Identification of matrix stiffness-related molecular subtypes in HCC via integrating multi-omics analysis and machine learning algorithms

doi: 10.1186/s12967-025-06733-7

Figure Lengend Snippet: The expression pattern and tissue localization of PPARG in tumor samples. ( A ) PPARG expression levels in tumor and normal samples of the TCGA dataset. ( B ) PPARG was correlated with pathological grades in the TCGA dataset. ( C ) Survival analysis of OS time between high and low-PPARG groups. ( D ) Survival analysis of DSS time between high and low-PPARG groups. ( E ) Correlation analyses between PPARG expression and tumor phenotypes. ( F , H , J ) PPARG expression in different cell types of spatial transcriptomics. F : LIHC1, H : LIHC2, J : LIHC3. ( G , I , K ) The comparisons of PPARG expression levels between malignant and normal samples. ( L ) The visualizations of the relationship between PPARG expression and various components of TME

Article Snippet: Spatial transcriptomics (ST) profiles were obtained from Mendeley Data (skrx2fz79n) [ ].

Techniques: Expressing