Journal: The Journal of Clinical Investigation

Article Title: The IFITM5 mutation in osteogenesis imperfecta type V is associated with an ERK/SOX9-dependent osteoprogenitor differentiation defect

doi: 10.1172/JCI170369

Figure Lengend Snippet: ( A – B ) Lineage tracing of chondrocytes coexpressing mutant Ifitm5 and Ai9 reporter in Rosa 26 mIfitm5/Ai9 Acan-Cre ERT2 mice. Tamoxifen injection was performed at P10, and bones were collected after 3 weeks (at 5 weeks of age). Representative images of the proximal tibia ( A ) and the tibia diaphyseal area ( B ) Decreased fraction of Ai9 + cells migrated to the bone diaphysis in mutant animals compared with littermate controls ( n = 3 per genotype; n = 2–3 fields counted per sample; * P = 0.03, by 2-tailed Student’s t test). Original magnification, ×20. ( C ) RNA-Seq of total femoral cDNA from Rosa26 mIfitm5/+ Acan-Cre ERT2 mice ( n = 3 per genotype) showed enrichment for chondrogenic gene expression in the mutant samples by GO term analysis. ( D ) Heatmap of focused differential gene expression analysis from RNA-Seq, showing upregulation of chondrogenic gene markers and decreased expression of osteogenic markers in the mutants compared with the control group.

Article Snippet: Differential gene expression analysis was performed using DESeq2, and statistical significance was determined by 2-way ANOVA, which is built into the Partek Genomics Suite RNA-Seq analysis pipeline.

Techniques: Mutagenesis, Injection, RNA Sequencing Assay, Expressing, Control

Journal: The Journal of Clinical Investigation

Article Title: The IFITM5 mutation in osteogenesis imperfecta type V is associated with an ERK/SOX9-dependent osteoprogenitor differentiation defect

doi: 10.1172/JCI170369

Figure Lengend Snippet: ( A – B ) Lineage tracing of chondrocytes coexpressing mutant Ifitm5 and Ai9 reporter in Rosa 26 mIfitm5/Ai9 Acan-Cre ERT2 mice. Tamoxifen injection was performed at P10, and bones were collected after 3 weeks (at 5 weeks of age). Representative images of the proximal tibia ( A ) and the tibia diaphyseal area ( B ) Decreased fraction of Ai9 + cells migrated to the bone diaphysis in mutant animals compared with littermate controls ( n = 3 per genotype; n = 2–3 fields counted per sample; * P = 0.03, by 2-tailed Student’s t test). Original magnification, ×20. ( C ) RNA-Seq of total femoral cDNA from Rosa26 mIfitm5/+ Acan-Cre ERT2 mice ( n = 3 per genotype) showed enrichment for chondrogenic gene expression in the mutant samples by GO term analysis. ( D ) Heatmap of focused differential gene expression analysis from RNA-Seq, showing upregulation of chondrogenic gene markers and decreased expression of osteogenic markers in the mutants compared with the control group.

Article Snippet: Normalization, differential expression, hierarchical clustering, and GO analysis were then performed using the RNA-Seq analysis pipeline in Partek Genomics Suite (Partek).

Techniques: Mutagenesis, Injection, RNA Sequencing Assay, Expressing, Control

Journal: Scientific Reports

Article Title: Digital pathology with artificial intelligence analysis provides insight to the efficacy of anti-fibrotic compounds in human 3D MASH model

doi: 10.1038/s41598-024-55438-2

Figure Lengend Snippet: Overview of FibroNest™ platform workflow for fibrosis quantification and MASH induction method. ( A ) FibroNest™ quantitative image analysis workflow and method. ( B ) Scheme for MASH induction in hLiMTs. Disease induction and treatment start at day 0 after the production of the hLiMTs. The three treatment conditions are: LEAN, MASH and MASH in the presence of test compounds. After each medium exchange on days 0, 3, 5 and 7, the compounds and vehicle controls (DMSO or PBS) were applied. FFAs supplementation occurred on each treatment day, while stimulation with LPS took place only once during the 10-day treatment period. Cell culture supernatants and/or microtissues were collected on days 5, 7 and 10. All the end points related to pro-collagen type I/III (pro-coll I/III), Histology/SR, TIMPs/matrix metalloproteinases (MMPs) and RNA sequencing (RNA-Seq) were performed on day 10. All conditions were normalized to 0.2% DMSO or PBS.

Article Snippet: The gene expression data were then analyzed with the InSphero RNA-Seq analysis pipeline.

Techniques: Cell Culture, RNA Sequencing Assay