Journal: Materials Today Bio
Article Title: Modeling a mesenchymal cell state by bioprinting for the molecular analysis of dormancy in melanoma
doi: 10.1016/j.mtbio.2025.101674
Figure Lengend Snippet: CIB culture induces a stable mesenchymal phenotype of Mel Im. Assignment of DEGs comparing CIB- and MG-cultured cells with published scRNA-Seq data of malignant melanoma . The cell state annotated marker genes described by Pozniak et al. were used to match the CIB specific gene signature composed of upregulated genes (LFC >1.5) with the validated cell clusters in human melanoma tumor biopsy samples. A) Significantly upregulated genes in CIB cultivated cells showed an enrichment in the neural crest like and mesenchymal defined cell clusters and B) significantly upregulated genes under MG culture conditions illustrate an enrichment in the mitotic cell cluster. C) Expression status of the respective marker genes of the mitotic, neural crest like and mesenchymal cell type clusters in CIB- and MG-cultured melanoma cells based on the scaled normalized RNA-Seq count data. D) CDKN1A RNA-Seq read counts (normalized to library size) in CIB- and MG-cultured Mel Im cells. E) CDKN1A (p21) mRNA expression analysis of Mel Im cultured in CIB or MG by qRT-PCR. F) Immunohistochemical staining for p21 on fixed and paraffin-embedded sections of CIB- or MG-cultured Mel Im. Scale bar = 100 μm. G) Representative images and quantification of Mel Im FUCCI after siPool mediated knockdown of p21 in CIB culture. Scale bar = 100 μm. H) KLF4 RNA-Seq read counts (normalized to library size) in CIB- and MG-cultured Mel Im cells. I) KLF4 mRNA expression analysis of Mel Im cultured in CIB or MG by qRT-PCR. J) Immunohistochemical staining for KLF4 on fixed and paraffin-embedded sections of CIB- or MG-cultured Mel Im. Scale bar = 100 μm. K) Representative images and quantification of Mel Im FUCCI after siPool mediated knockdown of KLF4 in CIB culture. Scale bar = 100 μm ∗p ≤ 0.05 ( D , E , H , I : Student's t-test. G , K : Two-way ANOVA followed by Bonferroni post-test).
Article Snippet: Immunohistochemical staining was performed as described previously, using primary antibodies anti-p21 (1:50, #2947, Cell Signaling, Danvers, MA, USA) or anti-KLF4 (1:500, HPA002926, Sigma Aldrich, St. Louis, MO, USA) [ ].
Techniques: Cell Culture, Marker, Expressing, RNA Sequencing, Quantitative RT-PCR, Immunohistochemical staining, Staining, Knockdown