Journal: Research

Article Title: Mapping Immune-Inflammatory Niches on Zirconia Bone Implants: Single-Cell Transcriptomic Profiling

doi: 10.34133/research.1162

Figure Lengend Snippet: Ti and ZrO 2 implants induce early osseointegration and immune inflammation. (A) Transcriptional levels of osteogenesis-related and immune-inflammatory genes. Osteogenic genes: Runx2 , Osterix , and Tgfb1 . Immune-inflammatory genes: Il1b , Mmp9 , and Il23a . (B) Receiver operating characteristic (ROC) analysis based on bulk RNA-seq data. AUC, area under the curve. (C) Protein expression levels of osteogenesis-related and immune-inflammatory markers. Osteogenic proteins: RUNX2, OSX, TGFB1, pSMAD2/SMAD2, and pSMAD3/SMAD3. Immune-inflammatory proteins: IL1B, MMP9, and IL23A. (D) Statistical analysis of protein expression levels. Statistical significance was determined using one-way analysis of variance. RUNX2, RUNX family transcription factor 2; OSX, osterix; TGFB1, transforming growth factor beta 1; SMAD2, SMAD family member 2; SMAD3, SMAD family member 3; IL1B, interleukin 1 beta; MMP9, matrix metallopeptidase 9; IL23A, interleukin 23 subunit alpha.

Article Snippet: The membranes were blocked with 5% nonfat milk for 1 h, followed by overnight incubation at 4 °C with the following primary antibodies: RUNX2 (Bioss, bs-1134R, 1:1,000, China), OSX (Bioss, bs-25532R, 1:1,000, China), pSMAD2 (Bioss, bs-3419R, 1:1,000, China), pSMAD3 (Bioss, bs-3425R, 1:1,000, China), IL1B (Bioss, bs-0812R, 1:1,000, China), MMP9 (Bioss, bsm-54040R, 1:3,000, China), IL23A (Bioss, bs-1193R, 1:1,000, China), NOS2 (Bioss, bs-0162R, 1:2,000, China), CD206 (Bioss, bsm-55604R, 1:1,000, China), TGFB1 (Proteintech, 81746-2-RR, 1:1,000, China), SMAD2 (Proteintech, 12570-1-AP, 1:3,000, China), and SMAD3 (Proteintech, 30130-1-AP, 1:2,000, China).

Techniques: RNA Sequencing, Expressing

Journal: Scientific Reports

Article Title: Celastrol attenuates Th1- and Th2-driven skin inflammation in 2D and 3D in vitro models

doi: 10.1038/s41598-026-47386-w

Figure Lengend Snippet: Determination of the relative mRNA expression of the proinflammatory marker CXCL8 ( a ), IL6 ( b ), IL1B ( c ), and IL23A ( d ) of the 3D AD models treated with 10µM celastrol (CS) on days 0, 6, and 12 of the airlift period (CS) compared to vehicle treated AD disease models (CTRL). Gene expression was measured using RT-qPCR. Values were plotted as log2 changes with log 2 (2) = 1 presenting a doubled upregulation and log 2 (0,5)=−1 presenting a downregulation by factor 2 compared to the control.

Article Snippet: IL23A , fw:5‘-GAATCAGGCTCAAAGCAAGTGG-3’ rev:5‘-AGCAACAGCAGCATTACAGC-3‘ , Eurofins.

Techniques: Expressing, Marker, Gene Expression, Quantitative RT-PCR, Control

Journal: bioRxiv

Article Title: Restoration of Keratinocyte Homeostasis Drives Resolution of Skin Inflammation

doi: 10.64898/2026.03.04.708224

Figure Lengend Snippet: a, Volcano plots depicting global differential gene expression across disease and restoration states. Left: KC-Tie2 versus C57BL/6 skin under control conditions, defining disease-associated transcriptional changes. Middle: KC-Tie2 skin following ω-3 PUFA exposure versus KC-Tie2 control skin, illustrating transcriptional changes accompanying disease normalization. Right: Subset of disease-associated genes that are significantly modulated in the opposite direction during ω-3 PUFA-mediated disease resolution. Genes were filtered using |log₂ fold change| ≥ 1.5 and FDR < 0.05; non-significant genes are shown in grey. Selected genes with large effect sizes are labeled. The transgene Tek and the epithelial regulators Serpinb3b , Slc25a5 , and Cacna2d1 are highlighted and examined further in subsequent figures. Summary statistics for all differential expression contrasts, including DEG counts and directionality, are provided in Supplementary Table 3. b, Expression of inflammatory mediators ( Il23a , Il17a , Tnf , Il22 , Il1f6 , and Il1f5 ) in dorsal skin from C57BL/6 and KC-Tie2 mice under control or ω-3 PUFA exposure. Data are shown as individual biological replicates with mean ± s.e.m. Statistical significance was determined by two-way ANOVA with Tukey’s post hoc testing; * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001; ns, not significant. c, KEGG pathway enrichment analysis of genes increased (upper) or decreased (lower) in KC-Tie2 skin relative to C57BL/6 controls (Disease Effect). Enrichment of cardiomyopathy and contractility-related annotations reflect overrepresentation of actin-myosin and calcium-handling genes that are shared across tissues. d, KEGG pathway enrichment analysis of genes decreased (upper) or increased (lower) during ω-3 PUFA-mediated restoration in KC-Tie2 skin (Disease Resolution), demonstrating bidirectional normalization of disease-associated pathways. Dot size represents gene count; color denotes odds ratio; the x-axis indicates −log₁₀(FDR). Full gene lists and enrichment statistics are provided in Supplementary Tables 4-7. e, Density plots of log₂ fold-change distributions for genes associated with basal, differentiated, and keratinized epidermal compartments. KC-Tie2 versus C57BL/6 skin under control conditions demonstrates disease-associated transcriptional shifts across epidermal layers (upper). ω-3 PUFA-exposed KC-Tie2 skin versus control-fed KC-Tie2 skin shows redistribution of effect sizes toward baseline (lower), indicating that both disease-associated dysregulation and its normalization are concentrated within epidermal gene programs. f, Schematic summary integrating transcriptional analyses across disease and resolution states. Chronic inflamed skin is characterized by coordinated activation of IL-17-driven inflammatory signaling, keratinocyte stress responses, disrupted lipid and fatty acid metabolism, and altered calcium and cytoskeletal programs. Disease resolution is associated with suppression of inflammatory modules alongside reactivation of epidermal differentiation, barrier formation, lipid metabolism, calcium signaling, and structural homeostasis, consistent with keratinocyte-centered, systems-level transcriptional reprogramming.

Article Snippet: Mouse primers (ThermoFisher Scientific) used in this study were: Il23a , Mm01160011_g1; Il17a , Mm00439618_m1; Il17c, Mm00521397_m1, Ccl20 , Mm00444228_m1; S100a8 , Mm00495696_g1; Tnf , Mm00443260_g1, Cacna2d1 , Mm00486607_m1; Serpinb3b , Mm03032256_uH; Slc25a5 , Mm00846873_g1; and Gapdh , Mm99999915_g1.

Techniques: Gene Expression, Control, Labeling, Quantitative Proteomics, Expressing, Activation Assay

Journal: bioRxiv

Article Title: Restoration of Keratinocyte Homeostasis Drives Resolution of Skin Inflammation

doi: 10.64898/2026.03.04.708224

Figure Lengend Snippet: a, Experimental schematic for topical siRNA-mediated gene silencing in KC-Tie2 mice. Non-targeting control siRNA or gene-specific siRNAs targeting Cacna2d1 , Serpinb3b , or Slc25a5 were applied topically to ear skin at the indicated time points, with tissue collection on day 14. b, Representative hematoxylin and eosin–stained sections of ear skin following treatment with control siRNA or gene-specific siRNAs. c, Heatmap summarizing changes in epidermal acanthosis and expression of IL-23/IL-17-axis-associated genes ( Il23a , Ccl20 , S100a8 , Il17a , Tnf , Il17c ) following gene-specific knockdown. Values are shown as log₂ fold change relative to control siRNA-treated skin. Acanthosis is coded as increased or decreased relative to control. d, Correlation heatmap relating each targeted gene to transcriptional programs identified by bulk RNA-seq pathway analyses, including fatty acid and lipid metabolism, epidermal barrier and junctional organization, IL-17-associated inflammatory signaling, epidermal differentiation and cornified envelope formation, cholesterol and sterol biosynthesis, and neutrophil activation/degranulation. Quantitative log₂ fold-change values underlying the cytokine and alarmin heatmap in c are provided in Supplementary Table 29.

Article Snippet: Mouse primers (ThermoFisher Scientific) used in this study were: Il23a , Mm01160011_g1; Il17a , Mm00439618_m1; Il17c, Mm00521397_m1, Ccl20 , Mm00444228_m1; S100a8 , Mm00495696_g1; Tnf , Mm00443260_g1, Cacna2d1 , Mm00486607_m1; Serpinb3b , Mm03032256_uH; Slc25a5 , Mm00846873_g1; and Gapdh , Mm99999915_g1.

Techniques: Control, Staining, Expressing, Knockdown, RNA Sequencing, Activation Assay