Journal: European Journal of Immunology

Article Title: Spatially Resolved Profiling of Compartmentalized Muscle and Brain Inflammation

doi: 10.1002/eji.70119

Figure Lengend Snippet: Conceptual framework for spatially informed tissue profiling. High‐throughput molecular phenotyping via single‐cell or single‐nucleus RNA sequencing enables the characterization of expression in each cell. Cell types or states can be clustered following dimensional reduction, most commonly UMAP. Individual genes or small subsets can be localized in spatial transcriptomic datasets. At the same time, transcriptional identities (like cell types) can be projected onto spatial maps, integrating both modalities. From there, several downstream applications may be used. Including Single gene validations using orthogonal imaging‐based methods like FISH or IHC Functionally validate spatial findings in culture models in vitro or in animal models in vivo Expand the analysis to incorporate other modalities (omics) that in turn may be integrated. Created with Biorender.com.

Article Snippet: High‐resolution spatial transcriptomic atlas of mouse soleus muscle: Unveiling single cell and subcellular heterogeneity in health and denervation , Jer‐En Hsu , 2024 (preprint) , Spatial Transcriptomics ( Seq‐Scope 3–7 dpi) paired with Histology , Mouse (6 months) , Denervation (surgical nerve removal) , Soleus (with and without sciatic nerve) , Novel hybrid fibers at a transitional state Mapped NMJ nuclei Fiber differences to stress and Denervation‐induced ECM remodeling dynamics.

Techniques: High Throughput Screening Assay, RNA Sequencing, Expressing, Imaging, In Vitro, In Vivo

Journal: bioRxiv

Article Title: Nucleosome stability safeguards cell identity, stress resilience and healthy aging

doi: 10.1101/2025.09.17.676776

Figure Lengend Snippet: a, Structural location of histone H2B residues D68 and E76 mutated in this study. H2B is shown in magenta, H4 in cyan. b, Nucleosome stability assessed by FRAP in IMR-90 SV40-T cells expressing EGFP-tagged H2B WT or mutants. Scale bar, 10 μm. Relative intensity was calculated by comparing the bleached site to the unbleached site. Data represent mean ± s.d. from >15 nuclei. The plateau value ( Ymax ) was calculated from the fitted recovery curve. P -values were calculated using unpaired, two-tailed Student’s t -tests comparing each mutant to WT at the final time point. c, Histone turnover in live cells assessed using SNAP-tagged H2B WT or mutants labeled with SNAP-TMR. Data represent mean ± s.d. of total field fluorescence from >2600 cells across three independent wells per condition. Half-life ( t 1/2 ) was calculated from the fitted decay curve. P -values were calculated using unpaired, two-tailed Student’s t -tests comparing each mutant to WT at the final time point. d, PCA of bulk mRNA-seq from skeletal muscle expressing H2B WT, mutants or empty vector. Each dot represents an individual mouse (n = 6, Empty; 5, WT; 4, D68N; 5, E76K; 5, E76R). e, GSEA of hallmark pathways in transduced skeletal muscle comparing each mutant to Empty and WT. (See for full pathways). f, IPA upstream regulator analysis showing suppression of Myod1- or Six1-associated genes and activation of Tnf- or Nfkb-associated genes across mutant-expressing skeletal muscle compared to Empty and WT. g, GSEA of Tabula Muris Senis aging signatures in transduced skeletal muscle comparing all mutants to Empty and WT. h, PCA of bulk mRNA-seq from heart expressing H2B WT, mutants or an empty vector. Each dot represents an individual mouse (n = 6, Empty; 5, WT; 4, D68N; 5, E76K; 5, E76R). i, GSEA of hallmark pathways in transduced heart comparing each mutant to Empty and WT. (See for full pathways). j, IPA upstream regulator analysis showing suppression of Ppara- or Ppargc1a-associated genes and activation of Tgfb1- or Smad3-associated genes across mutant-expressing heart compared to Empty and WT. k, GSEA of Tabula Muris Senis aging signatures in transduced heart comparing all mutants to Empty and WT. l, Schematic of experimental design. MSCV-based retroviral vectors expressing H2B WT or mutants were introduced into HSPCs (Lin⁻Sca-1⁺c-Kit⁺), and myeloid or megakaryocyte/erythroid differentiation was assessed. m, GSEA of hallmark pathways in transduced HSPCs comparing each mutant to Empty and WT. (See for full pathways). n, IPA upstream regulator analysis showing suppression of Cebpa- or Cebpb-associated genes (myeloid regulators) and activation of Gata1- or Gata2-associated genes (megakaryocyte/erythroid regulators) in mutant-expressing HSPCs 9 days after differentiation. o, GSEA of cell type signatures indicating increased megakaryocyte and erythroid lineage features and decreased myeloid (neutrophil, monocyte and macrophage) features in mutant-expressing cells compared to Empty and WT.

Article Snippet: Cell type signature profiles using the mouse aging cell atlas, Tabula Muris Senis , revealed that mutant-expressing skeletal muscle recapitulated aging-like transcriptional signatures across macrophages, T cells, muscle satellite cells, mesenchymal stem cells and B cells ( ).

Techniques: Expressing, Two Tailed Test, Mutagenesis, Labeling, Fluorescence, Plasmid Preparation, Activation Assay, Retroviral