workflow  (Amira Pharmaceuticals)

Journal: Science Advances

Article Title: Lineage master regulator and cancer-selective partner transcription factors rewire 3D genome topology for tumor-specific gene control

doi: 10.1126/sciadv.adz9441

Figure Lengend Snippet: ( A ) Schematic of multi-omics analysis of scrambled control (CTRLi) and p63 knockdown (p63i) in SCC cell lines and normal undifferentiated and differentiated keratinocytes. Created in BioRender. Jung, N. (2026) https://BioRender.com/nxxtu3u . ( B ) Dot plot of significant pathways from gene ontology (GO) analysis of p63-dependent genes identified through RNA-seq. Undifferentiated keratinocytes (Undiff) and differentiated keratinocytes (Diff) are indicated. p63-related features in SCC cells compared to normal keratinocytes were classified into four classes: (i) SCC-specific, (ii) shared between SCC and undifferentiated keratinocytes (SCC & Undiff), (iii) shared between SCC and differentiated keratinocytes (SCC & Diff), and (iv) shared by SCC, undifferentiated, and differentiated keratinocytes (all common). ( C ) Peak-centered ChIP-seq heatmaps of four classes of p63 binding sites in SCC cells compared to normal keratinocytes and ATAC-seq heatmap corresponding to the ChIP-seq peaks. ( D ) Venn diagram comparing CAL27 and SCC13 cell line-specific p63 binding sites (permutation test). ( E ) Bar plot of distances between transcriptional start site (TSS) of potential target genes in the cell cycle pathway and common SCC cell line-specific p63 binding sites. ( F ) Heatmaps of four classes of p63-dependent chromatin accessibility, compared to normal keratinocytes. ( G ) Venn diagram comparing CAL27 and SCC13 cell line-specific p63-dependent chromatin accessibility. ( H ) Bar plot showing the distances between TSS of potential target genes in the cell cycle pathway and common SCC cell line-specific p63-dependent chromatin accessibility. ( I ) Track plot of MYC locus in SCC cells and normal human keratinocytes.

Article Snippet: Briefly, total RNA was extracted from CAL27 control and FOXK1 KO cells and submitted to Plasmidsaurus for library preparation and sequencing according to the provider’s standard RNA-seq workflow.

Techniques: Biomarker Discovery, Control, Knockdown, RNA Sequencing, ChIP-sequencing, Binding Assay

Journal: Science Advances

Article Title: Lineage master regulator and cancer-selective partner transcription factors rewire 3D genome topology for tumor-specific gene control

doi: 10.1126/sciadv.adz9441

Figure Lengend Snippet: ( A ) Principal component analysis (PCA) of H3K27ac HiChIP datasets. ( B ) Bar plot showing the proportion of enhancer-to-enhancer (E-E), enhancer-to-promoter (E-P), and promoter-to-promoter (P-P) interactions within p63-dependent chromatin loops. ( C ) Box plot showing the distances of p63-dependent loops in each cell type (Kruskal-Wallis test, followed by Dunn’s test adjusted with the Benjamini-Hochberg correction). ( D ) Dot plot showing enrichment of SCC-cell line-specific p63 binding or p63-dependent chromatin accessibility in p63-dependent loops, comparing CAL27 SCC cells to normal keratinocytes. ( E ) Heatmap of p63-dependent loops in CAL27 categorized into four classes, compared to normal keratinocytes. ( F ) Bar plot illustrating SCC cell line-specificity at the loop and anchor level in CAL27. ( G ) Dot plot showing the enrichment between SCC cell line-specific p63 binding or p63-dependent chromatin accessibility and the cell-type specific anchors consisting of the p63-dependent loops in CAL27 and the normal keratinocytes. ( H ) Dot plot showing the enrichment of p63-dependent chromatin loop’s target genes across four different RNA classes between CAL27 and normal keratinocytes. ( I ) Dot plot of significant pathways identified from GO analysis of common p63-dependent genes between SCCs and normal keratinocytes in CAL27 and SCC13 cells. ( J and K ) Top: virtual 4C plot. Bottom: bar plot showing normalized RNA-seq counts in CAL27 and normal keratinocytes. PTHLH (J) and SFN (K). Yellow box: an anchor connected to the target gene promoter. Fisher’s exact test with Bonferroni correction, one-sided applied to all the enrichment tests.

Article Snippet: Briefly, total RNA was extracted from CAL27 control and FOXK1 KO cells and submitted to Plasmidsaurus for library preparation and sequencing according to the provider’s standard RNA-seq workflow.

Techniques: HiChIP, Binding Assay, RNA Sequencing

Journal: Science Advances

Article Title: Lineage master regulator and cancer-selective partner transcription factors rewire 3D genome topology for tumor-specific gene control

doi: 10.1126/sciadv.adz9441

Figure Lengend Snippet: ( A ) Zipf plot showing connectivity per anchor of p63-dependent loops in CAL27 SCC cells and normal keratinocytes. ( B ) Box plot comparing connectivity of anchors without (NO) and with (YES) p63 binding or p63-dependent chromatin accessibility in CAL27 SCC cells and normal keratinocytes (Mann-Whitney U test). ( C ) Heatmap depicting connectivity across expansion, reduction, and stable groups (left), featuring z-scores of log 2 fold change (middle) and anchor classes (right) in a comparison between CAL27 SCC cells and undifferentiated keratinocytes. ( D ) Bar plot showing the proportion of anchors in expansion, reduction, and stable groups in comparisons between CAL27 SCC cells and normal keratinocytes. ( E ) GO terms for p63-dependent genes in the expansion group. ( F ) Survival analysis for HNSCC and CESC using genes from the expansion and reduction groups in CAL27 SCC cells versus undifferentiated keratinocytes. ( G ) Example of a gene in the expansion group, DSN1 ; lines represent chromatin looping. Circles and squares denote different anchors. The numbers indicate specific anchors. ( H ) Left: track plot with chromatin loops in CAL27 SCC cells and undifferentiated keratinocytes. Yellow: CAL27-specific anchors connected to DSN1 promoter, light blue: an anchor containing DSN1 promoter, light pink: common anchors between CAL27 and undifferentiated keratinocytes, connected to DSN1 promoter. Right: bar plot of normalized RNA-seq counts of DSN1 .

Article Snippet: Briefly, total RNA was extracted from CAL27 control and FOXK1 KO cells and submitted to Plasmidsaurus for library preparation and sequencing according to the provider’s standard RNA-seq workflow.

Techniques: Binding Assay, MANN-WHITNEY, Comparison, RNA Sequencing

Journal: Science Advances

Article Title: Lineage master regulator and cancer-selective partner transcription factors rewire 3D genome topology for tumor-specific gene control

doi: 10.1126/sciadv.adz9441

Figure Lengend Snippet: ( A ) Schematic of Promoter, Primary, and Secondary modes. ( B ) Bar plot showing the proportion of each regulation. ( C ) Error plot comparing log 2 fold change (p63i/CTRLi) in the regulatory modes in CAL27 SCC cells and undifferentiated keratinocytes (Kruskal-Wallis test, followed by Dunn’s test adjusted with the Benjamini-Hochberg correction). ( D and E ) Tile plot depicting the association between the regulatory modes and four classes of p63-dependent genes (D) and p63 binding sites (E) (Fisher’s exact test with Bonferroni correction, one-sided). ( F ) Example of Promoter mode: S100A2 . Top: p63 ChIP-seq track, bottom: bar plot showing normalized RNA-seq counts of S100A2 . ( G ) Example of Secondary mode in CAL27: CKAP5 . Top: tracks for p63 binding and H3K27ac HiChIP, bottom: bar plot showing normalized RNA-seq counts of CKAP5 . ( H ) Model of p63 regulatory programs in normal keratinocytes and SCCs.

Article Snippet: Briefly, total RNA was extracted from CAL27 control and FOXK1 KO cells and submitted to Plasmidsaurus for library preparation and sequencing according to the provider’s standard RNA-seq workflow.

Techniques: Binding Assay, ChIP-sequencing, RNA Sequencing, HiChIP

Journal: Clinical, Cosmetic and Investigational Dermatology

Article Title: Exosomes in Psoriasis: From Pathogenic Mechanisms to Therapeutic Innovations

doi: 10.2147/CCID.S606845

Figure Lengend Snippet: Proposed workflow for exosome‑based clinical diagnostics in psoriasis. The workflow follows MISEV2023 guidelines and includes (1) sample collection (plasma, urine or tissue, processed on ice within 1 h); (2) EV separation (differential ultracentrifugation plus iodixanol density gradient); (3) orthogonal quality control (NTA, TEM, EV markers CD9/CD63/CD81/ALIX/TSG101, and exclusion of non‑EV contaminants such as calnexin); (4) molecular profiling (qRT‑PCR or ddPCR for exosomal miRNAs or mRNAs); and (5) clinical interpretation (ROC‑derived cut‑offs, composite scores with PASI/CRP, independent validation). No exosome‑based psoriasis test has yet received regulatory clearance.

Article Snippet: Exosome diagnostic workflow for psoriasis: 5 steps from collection to validation.

Techniques: Clinical Proteomics, Control, Biomarker Discovery