Journal: bioRxiv

Article Title: BAF complex-independent gene activation by SS18::SSX

doi: 10.64898/2026.01.26.701739

Figure Lengend Snippet: (A) Left: Immunofluorescence of HEK293T cells expressing wild-type SS18::SSX1 (FL) treated for 72h with either 500nM ACBI1 or 500nM dCBP- 1 (cyan) stained for H2AK119ub1 (H2Aub) (magenta). Images are representative of n = 2 biological replicates. Scale bar, 5 μm. Right: profile of fluorescence intensity of FL, treated for 72h with either 500nM ACBI1 or 500nM dCBP-1 over H2Aub or eGFP foci. Data represent the mean ± S.E.M of n = 2 biological replicates. For each replicate and condition, > 10 foci where profiled. R² indicates Pearson correlation coefficient. (B) Left: Immunofluorescence of HEK293T cells expressing eGFP or wild-type SS18::SSX1, either untreated (FL) (cyan) or treated for 72h with 500nM ACBI1 or 500nM dCBP-1 stained for SMARCC1 (magenta). Images are representative of n = 2 biological replicates. Scale bar, 5 μm. Right: Profile of fluorescence intensity. Data represent the mean ± S.E.M of n = 2 biological replicates. For each replicate, > 10 foci where profiled. R² indicates Pearson correlation coefficient.

Article Snippet: The SMARCA2/SMARCA4 degrader ACBI1 (2375564-55-7) and the EP300/CREBBP degrader dCBP-1 (2484739-25-3) were purchased from MedChemExpress, resuspended in dimethyl sulfoxide (DMSO) and kept at −80°C.

Techniques: Immunofluorescence, Expressing, Staining, Fluorescence

Journal: bioRxiv

Article Title: BAF complex-independent gene activation by SS18::SSX

doi: 10.64898/2026.01.26.701739

Figure Lengend Snippet: (A) Left: Immunofluorescence of HEK293T cells expressing eGFP or wild-type SS18::SSX1, either untreated (FL) (cyan) or treated for 72h with 500nM ACBI1 or 500nM dCBP-1 stained for EP300 (magenta). Images are representative of n = 2 biological replicates. Scale bar, 5 μm. Right: Profile of fluorescence intensity. Data represent the mean ± S.E.M of n = 2 biological replicates. For each replicate, > 10 foci where profiled. R² indicates Pearson correlation coefficient. (B ) Western Blot of KHOS-240S whole cell extracts treated for 24h with DMSO, 500nM or 1uM dCBP- 1 revealed using EP300, CREBBP or β-actin antibodies. (C) RNA-seq heatmap showing the 1,000 most variable genes with a cutoff z-score of 4 from KHOS-240S cells expressing eGFP or SS18::SSX1 (FL) treated for 72h with either DMSO, 500nM ACBI1 or 500nM dCBP-1. n = 2 biological replicates. ( D) Log2-transformed fold change of FPKM values in KHOS-240S RNA-seq relative to eGFP over selected SS18::SSX target genes. Data represents the mean. (E) Scatter plot of log2-transformed fold change of FPKM values in KHOS-240S RNA-seq relative to eGFP over genes up-regulated by SS18::SSX1 expression and showing >2 fold up-regulation. Biological replicates are combined using their mean. Bold line represents median and dotted line represents cutoff of 2. (F) RNA-seq heatmap showing the 1,000 most variable genes with a cutoff z-score of 4 from wild-type hMSC or cells expressing eGFP-SSX1, eGFP-SS18::SSX1 isoform1, eGFP-SS18::SSX1 isoform2, eGFP-EWSR1::SSX1 or eGFP- EPC1::SSX1 treated for 48h with 500nM dCBP-1. n = 2 biological replicates. (G) Top: Immunofluorescence of HEK293T cells expressing wild-type eGFP-SSX1, eGFP-SS18::SSX1 isoform1, eGFP-SS18::SSX1 isoform2, eGFP-EWSR1::SSX1 or eGFP-EPC1::SSX1(cyan) stained for EP300 (magenta). Images are representative of n = 2 biological replicates. Scale bar, 5 μm. Bottom: profile of fluorescence intensity of eGFP constructs over SSX-rich eGFP foci. Data represent the mean ± S.E.M of n = 2 biological replicates. For each replicate and condition, > 10 foci where profiled. R² and r indicate Pearson correlation coefficients. (H) Scatter plot of log2-transformed fold change of CPM values in hMSC RNA-seq relative to untreated hMSC over the union genes up-regulated by SS18::SSX1 isoform1 (log2FC >2) and up-regulated by EPC1::SSX1 (log2FC >1). Biological replicates are combined using their mean. Bold line represents median. (I) Log2-transformed fold change of CPM values in hMSC RNA-seq relative to untreated cells over selected SSX target genes. Data represents the mean. (J) qRT-PCR displaying log2- transformed fold change of mRNA levels normalised by GAPDH in HSSY-II, SYO-1, CME-1 and Yamato-SS cells treated for 72h with 500nM dCBP-1 relative to DMSO. Data represents the mean of n = 2 biological replicates. (K) Viability of 4 synovial sarcoma cell lines (Yamato-SS, SYO-1, CME-1, HSSY-II) and KHOS-240S osteosarcoma cells treated with various concentrations of dCBP-1. The symbols represent the mean ± S.E.M of n = 3 biological replicates, the solid line represent the nonlinear curve fitting and its associated IC50. p-value represents extra sum-of- squares F test between KHOS-240S and SYO-1 nonlinear regression curves.

Article Snippet: The SMARCA2/SMARCA4 degrader ACBI1 (2375564-55-7) and the EP300/CREBBP degrader dCBP-1 (2484739-25-3) were purchased from MedChemExpress, resuspended in dimethyl sulfoxide (DMSO) and kept at −80°C.

Techniques: Immunofluorescence, Expressing, Staining, Fluorescence, Western Blot, RNA Sequencing, Transformation Assay, Construct, Quantitative RT-PCR

Journal: bioRxiv

Article Title: Quantitative dissection of the metastatic cascade at single colony resolution

doi: 10.64898/2026.02.20.706841

Figure Lengend Snippet: CREBBP suppresses SCLC metastasis through regulating Cdx2 expression. a. UMAP of single-nucleus RNA-seq from Crebbp- WT and Crebbp- KO liver metastases showing four Ascl1⁺ SCLC clusters. Crebbp- KO metastases are enriched in cluster 4 SCLC. Left, UMAP for combined samples with all cell type identified. A total of 55,558 nuclei were analyzed. Right-Top, UMAP for SCLC clusters identified in Crebbp- WT sample with Asc1 UMI >1 per cell. Right-Bottom, UMAP for SCLC clusters identified in Crebbp -KO sample with Asc1 UMI >1 per cell. b. Alluvial plot showing cluster composition of Ascl1 ⁺ SCLC cells from Crebbp- WT and Crebbp- KO liver metastases. Crebbp- KO samples are dominated by Cluster 4 SCLC cells, comprising over 70% of the population. c. Cluster 4 SCLC displays MYC signaling activation. Gene set enrichment analysis (GSEA) of Ascl1 ⁺ SCLC clusters, with circle color indicating enrichment z-score and size reflecting the percentage of genes enriched in each pathway. d. Crebbp- KO SCLC cells exhibit increased proliferation and loss of neuroendocrine identity. Violin plots showing pairwise comparisons of S- and G2/M-phase scores and neuronal scores across the four SCLC clusters in Crebbp- WT and Crebbp- KO metastases. e. Schematic of co-transplantation experiment for bulk RNAseq. GFP-labeled Crebbp- WT and mCherry-labeled Crebbp- KO RP48 cells were mixed at a 1:1 ratio and transplanted via tail vein injection. After 3 weeks, liver metastases were dissociated, and GFP⁺ and mCherry⁺ SCLC cells were isolated by FACS for bulk RNA-seq analysis. PCA plot shows a well separation between WT and KO samples. f. Volcano plot showing differentially expressed genes between Crebbp- WT and Crebbp -KO metastatic SCLC cells. A total of 459 genes were upregulated (>2-fold) in Crebbp- KO cells, while 474 genes were upregulated (>2-fold) in Crebbp- WT cells, indicating balanced transcriptional activation and repression upon Crebbp loss. g. GSEA analysis of bulk RNA-seq from sorted Crebbp- WT and Crebbp- KO SCLC cells showing loss of neuroendocrine programs and activation of type I interferon signaling in Crebbp- KO cells. Circle color represents enrichment FDR, and circle size reflects the number of genes contributing to each pathway. h. Integration of H3K27Ac ChIP-seq and RNA-seq identifies Cdx2 as a direct CREBBP target. Differential H3K27Ac peak signals between Crebbp- WT and Crebbp -KO SCLC cells (two biological replicates) were cross-compared with differential gene expression from RNA-seq. Circle color represents –log₁₀FDR, and circle size reflects the total number of differential peaks per gene. Cdx2 is among the most significantly enriched and shared targets in WT cells comparing to KO cells. i. Crebbp loss specifically reduces H3K27Ac modification at the Cdx2 locus. H3K27Ac ChIP-seq tracks from Crebbp- WT and Crebbp- KO SCLC cells are shown for the indicated chromosome 5 region. Crebbp- KO cells display a selective loss of H3K27Ac at the Cdx2 locus, while neighboring gene loci remain unaffected. j. Crebbp l oss diminished CDX2 protein expression in SCLC cells. Western blot analysis of CREBBP, CDX2, and H3K27Ac in Crebbp- WT and Crebbp- KO RP48 cells. Total H3 and GAPDH are blotted as control. k. Doxycycline-induced CDX2 re-expression in Crebbp- KO RP48 cells suppresses proliferation and growth advantage in co-culture with Crebbp- WT cells. Crebbp- WT-TetON-CDX2 and Crebbp- KO-TetON-CDX2 RP48 cells were mixed at a 1:1 ratio and treated with 0, 100, or 500 ng/mL doxycycline in co-culture for 6 days. GFP/mCherry cell ratios were quantified by flow cytometry. n= 7 wells l. Schematic of the MOBA-seq screen using control or CDX2-overexpressing RP48 cells. Lentiviral sgRNA libraries were constructed using control (PuroR) or CDX2-overexpression (PuroR-2A-CDX2) backbones. 4N-barcoded control and CDX2-overexpressing RP48 cell libraries were mixed at a 1:1 ratio and transplanted via tail vein into five NGS mice. Three weeks post-transplantation, metastasis-bearing livers and lungs were collected, and over 20,000 barcoded metastases were identified from both tissues for MOBA-seq analysis. m. Crebbp-mediated metastatic suppression in the liver is CDX2-dependent. MOBA-seq analysis deconvoluted control and CDX2-overexpressing RP48 cells using their 4N-static barcodes. Genotype-specific metastatic burden was calculated as fold change relative to the mean of all control colonies ( sgCtrl ). The blue regression line with confidence interval represents genotypes unaffected by CDX2 expression, while those preferentially suppressed under CDX2-overexpressing conditions are highlighted in yellow. Crebbp inactivation increased liver metastatic burden only in control RP48 cells, but not in CDX2-overexpressing RP48 cells. n. Crebbp -mediated metastatic suppression in the lung is CDX2-dependent. MOBA-seq analysis of genotype-specific metastatic burden in control and CDX2-overexpressing RP48 cells that metastasized to the lung as described in m. Crebbp inactivation markedly increased lung metastatic burden in control RP48 cells but had a reduced effect in CDX2-overexpressing RP48 cells.

Article Snippet: Antibodies used in this study: GAPDH (Cell Signaling, 5174S, 1:2000), CREBBP (Cell Signaling, 7389S, 1:200), H3 (Cell Signaling, 4499S, 1:1000), CDX2 (Invitrogen, MA5-35215, 1:2000), H3K27Ac (Cell Signaling, 8173S, 1:1000), Goat-anti-Rabbit IgG Antibody, HRP-conjugate (Sigma-Aldrich, 12-348), Goat-anti-Mouse IgG Antibody, HRP-conjugate (Thermo Fisher Scientific, 62-6520).

Techniques: Expressing, RNA Sequencing, Activation Assay, Transplantation Assay, RNA sequencing, Labeling, Injection, Isolation, ChIP-sequencing, Gene Expression, Modification, Western Blot, Control, Co-Culture Assay, Flow Cytometry, Construct, Over Expression

Journal: bioRxiv

Article Title: Quantitative dissection of the metastatic cascade at single colony resolution

doi: 10.64898/2026.02.20.706841

Figure Lengend Snippet: a. Gene set enrichment analysis (GSEA) of snRNA-seq from Crebbp -WT and Crebbp -KO RP48 SCLC liver metastases. Heatmaps show normalized enrichment scores (KO vs. WT) across major cancer- and stroma-associated transcriptional programs. Crebbp loss leads to upregulation of MYC- and cell-cycle–associated signaling pathways. b. Transcriptome-wide correlation between differential gene expression measured by bulk RNA-seq and snRNA-seq. A moderate Pearson correlation (r = 0.51) indicates substantial concordance between mRNA- and pre-mRNA based expression changes across platforms. c. Heatmap of bulk RNA-seq profiles for the top 500 differentially expressed genes from sorted Crebbp -WT and Crebbp -KO RP48 SCLC liver metastases. Clustering reveals the emergence of distinct transcriptional status upon Crebbp loss, including marked downregulation of Cdx2 in Crebbp -KO cells. d. Pie charts summarizing differential H3K27ac ChIP-seq peaks identified in Crebbp -WT and Crebbp -KO cells. e. Doxycycline-induced CDX2 re-expression in Crebbp -KO RP48 cells suppresses proliferation and growth advantage in co-culture with Crebbp -WT cells. Crebbp -WT-TetON-CDX2 and Crebbp -KO-TetON-CDX2 RP48 cells were mixed at a 1:1 ratio and treated with 100ng/mL doxycycline in co-culture for 0, 4, and 8 days. GFP/mCherry cell ratios were quantified by flow cytometry. n= 6 wells f. Doxycycline-induced CDX2 re-expression in Crebbp -KO RP48 cells suppresses transwell migration in co-culture with Crebbp -WT cells. Crebbp -WT-TetON-CDX2 and Crebbp -KO-TetON-CDX2 RP48 cells were mixed at a 1:1 ratio and treated with 100ng/mL doxycycline for 4 days for transwell migration. GFP/mCherry cell ratios were quantified by flow cytometry. n= 6 wells g. Crebbp -mediated metastatic seeding suppression is CDX2-dependent. MOBA-seq analysis of genotype-specific metastatic seeding in control and CDX2-overexpressing RP48 cells that metastasized to the lung and liver. Crebbp inactivation increased metastatic seeding in control RP48 cells but had no effect in CDX2-overexpressing RP48 cells. h. Crebbp -mediated metastatic clonal expansion is CDX2-independent. MOBA-seq analysis of genotype-specific clonal expansion (90 th percentile colony size) in control and CDX2-overexpressing RP48 cells that metastasized to the lung and liver. Crebbp inactivation increased metastatic clonal expansion in both control and CDX2-overexpressing RP48 cells.

Article Snippet: Antibodies used in this study: GAPDH (Cell Signaling, 5174S, 1:2000), CREBBP (Cell Signaling, 7389S, 1:200), H3 (Cell Signaling, 4499S, 1:1000), CDX2 (Invitrogen, MA5-35215, 1:2000), H3K27Ac (Cell Signaling, 8173S, 1:1000), Goat-anti-Rabbit IgG Antibody, HRP-conjugate (Sigma-Aldrich, 12-348), Goat-anti-Mouse IgG Antibody, HRP-conjugate (Thermo Fisher Scientific, 62-6520).

Techniques: Protein-Protein interactions, Gene Expression, RNA Sequencing, Expressing, ChIP-sequencing, Co-Culture Assay, Flow Cytometry, Migration, Control