healthy control embryonic mouse fibroblast cells  (ATCC)

Journal: bioRxiv

Article Title: RUNX1 is Expressed in a Subpopulation of Dermal Fibroblasts and Higher RUNX1 Levels are Associated with the Severity of Systemic Sclerosis

doi: 10.1101/2024.04.03.587966

Figure Lengend Snippet: (A) RUNX1 expression rate in forearm skin biopsies of dcSSc ( N =49), lcSSc ( N =17), and healthy ( N =20) patients. (B) The expression rate of RUNX1 over the course of three years (data presented for 0, 6, 12, 24, and 36 months). (C) RUNX1 expression rate for healthy and SSc patients at early or late stages of disease at baseline. (D) Correlation between RUNX1 expression and mRSS skin score at baseline for both lcSSc (yellow) and dcSSc (red) ( N =66); early-stage patients are shown as a triangle and late-stage patients as a circle. (E) GSVA enrichment scores of main cellular signatures in healthy ( N =20), patients with RUNX1 high ( N =21) and RUNX1 low ( N =45). Hedge’s g effect size of RUNX1 high vs. RUNX1 low is presented in the graph. (F) Correlation between the TGF-β fibroblast and monocyte and myeloid cell signatures with RUNX1 .

Article Snippet: We analyzed a DNA microarray dataset previously generated by our lab, consisting of two independent SSc fibroblasts, one healthy control fibroblast isolated in parallel, and one normal human dermal (NHD) fibroblast cell lines obtained from ATCC.

Techniques: Expressing

Journal: bioRxiv

Article Title: RUNX1 is Expressed in a Subpopulation of Dermal Fibroblasts and Higher RUNX1 Levels are Associated with the Severity of Systemic Sclerosis

doi: 10.1101/2024.04.03.587966

Figure Lengend Snippet: (A) Schematic graph illustrating the timeline for the culture and TGF-β1 treatment of dcSSc-isolated fibroblasts, matched healthy-isolated fibroblasts, and Normal Human Dermal (NHD) fibroblast cells. (B) RUNX1 expression rate in samples treated with TGF-β1 (in red) vs. control for the 24 hours after exposure. (C) Volcano plot of differentially expressed analysis of the two SSc-isolated fibroblast lines at 12 hours after exposure vs. the baseline. (D) The pathway analysis of Reactome gene sets shows the biological pathways and processes that are significantly represented within top DEG genes of SSc-isolated fibroblast lines 12 hours after TGF-β1 treatment vs. the baseline. (E) Fold change expression of TGF-β1 and CBFB in TGF-β1-induced SSc fibroblasts treated with Ro5-3335 ( RUNX1 inhibitor), compared to control. (F) Proliferation curve of NHD fibroblasts in the presence and absence of Ro5-3335. (G–H) The 3D collagen contraction assays, fixed (G) and floating ( H ) models, of NHD fibroblasts treated with Ro5-3335. SIS3 (SMAD3 inhibitor) was used as positive control that significantly eliminates the contraction ability of fibroblasts. (Student’s t-test P- value: **0.001–0.01, ****<0.0001 in GraphPad Prism v9)

Article Snippet: We analyzed a DNA microarray dataset previously generated by our lab, consisting of two independent SSc fibroblasts, one healthy control fibroblast isolated in parallel, and one normal human dermal (NHD) fibroblast cell lines obtained from ATCC.

Techniques: Isolation, Expressing, Control, Positive Control

Journal: bioRxiv

Article Title: RUNX1 is Expressed in a Subpopulation of Dermal Fibroblasts and Higher RUNX1 Levels are Associated with the Severity of Systemic Sclerosis

doi: 10.1101/2024.04.03.587966

Figure Lengend Snippet: (A) THBS1 and RUNX1 expression levels in dcSSc skin biopsies of patients who were given two low doses (1 mg/kg) of fresolimumab at weeks 1 and 3 in yellow ( N =7); or a single high dose (5 mg/kg) of fresolimumab at week 1 in blue ( N =7). The mid-forearm skin biopsies were collected at baseline and again at weeks 3, 7, and 24. (B) The heatmap of genes in the TGF-β fibroblast cell signature for patients who received a high dose of fresolimumab at baseline and again 3 weeks after treatment ( N =7). (C) The expression of several genes including RUNX1 and TGF-β pathway biomarkers such as COMP , THBS1 , and FN1 .

Article Snippet: We analyzed a DNA microarray dataset previously generated by our lab, consisting of two independent SSc fibroblasts, one healthy control fibroblast isolated in parallel, and one normal human dermal (NHD) fibroblast cell lines obtained from ATCC.

Techniques: Expressing

Journal: bioRxiv

Article Title: RUNX1 is Expressed in a Subpopulation of Dermal Fibroblasts and Higher RUNX1 Levels are Associated with the Severity of Systemic Sclerosis

doi: 10.1101/2024.04.03.587966

Figure Lengend Snippet: (A) DNA methylation profile of 2D- and 3D-cultured fibroblasts isolated from dcSSc patients or healthy donors, created using Illumina’s Infinium Methylation EPIC array. Heatmap shows top 592 methylated CpG sites, with blue/yellow gradient of beta values. The bar-plot on top shows RUNX1 beta value that is labeled within the heatmap, showing that RUNX1 is hypomethylated in dcSSc samples. (B) Result of paired-wise differentially methylated CpGs and the number of significant CpGs in each group. (C) Pathway enrichment analysis of Reactome gene sets using top significant CpGs identified in (B) for each 2D and 3D culture. (D) The beta values of representative CpGs in RUNX1 locus in 2D and 3D SSc and healthy conditions. (E) RUNX1 locus on chromosome 21 and common CpG islands in green. The differentially methylated regions (DMRs) are identified between SSc and healthy samples are shown in red. The beta values corresponding to the CPGs at DMRs for SSc (in orange) and healthy (in green).

Article Snippet: We analyzed a DNA microarray dataset previously generated by our lab, consisting of two independent SSc fibroblasts, one healthy control fibroblast isolated in parallel, and one normal human dermal (NHD) fibroblast cell lines obtained from ATCC.

Techniques: DNA Methylation Assay, Cell Culture, Isolation, Methylation, Labeling

Journal: bioRxiv

Article Title: RUNX1 is Expressed in a Subpopulation of Dermal Fibroblasts and Higher RUNX1 Levels are Associated with the Severity of Systemic Sclerosis

doi: 10.1101/2024.04.03.587966

Figure Lengend Snippet: (A) UMAP projection of cell types from Tabib et al., 2021’s scRNA-seq of forearm skin biopsies (B) RUNX1 -normalized aggregate expression of 10 samples from healthy donors and 12 from dcSSc patients. (C) UMAP projection of 10 fibroblast subpopulations (clusters 0–9). Two fibroblast populations of 2 and 4 are marked, which are enriched SSc samples. (D) Feature plots of RUNX1 expression in healthy and SSc fibroblasts. Two RUNX1 -expressing fibroblast clusters are marked with their respective numbers. (E) The log-normalized expression rate of main differentially expressed genes between RUNX1 high - with RUNX1 low -expressing SSc fibroblasts. (F) Density plots of RUNX1 and major SSc-relevant genes within SSc fibroblast subpopulations. Arrows indicate the cluster 2 and 4 of SSc-specific subpopulations of fibroblasts.

Article Snippet: We analyzed a DNA microarray dataset previously generated by our lab, consisting of two independent SSc fibroblasts, one healthy control fibroblast isolated in parallel, and one normal human dermal (NHD) fibroblast cell lines obtained from ATCC.

Techniques: Expressing