Supplementary Figures S1 - S14 from <i>CREBBP</i> Inactivation Promotes the Development of HDAC3-Dependent Lymphomas
Authors: Jiang Yanwen , Ortega-Molina Ana , Geng Huimin , Ying Hsia-Yuan , Hatzi Katerina , Parsa Sara , McNally Dylan , Wang Ling , Doane Ashley S. , Agirre Xabier , Teater Matt , Meydan Cem , Li Zhuoning , Poloway David , Wang Shenqiu , Ennishi Daisuke , Scott David W. , Stengel Kristy R. , Kranz Janice E. , Holson Edward , Sharma Sneh , Young James W. , Chu Chi-Shuen , Roeder Robert G. , Shaknovich Rita , Hiebert Scott W. , Gascoyne Randy D. , Tam Wayne , Elemento Olivier , Wendel Hans-Guido , Melnick Ari M. 
Published: April 2023

<p>Supplementary Figure S1. Crebbp deficiency results in accelerated germinal center derived B-cell lymphoma development in mice. Supplementary Figure S2. Ep300 deficiency results in accelerated germinal center derived B-cell lymphoma development in mice. Supplementary Figure S3. Western blots showing the knockdown efficiency of shRNAs against human CREBBP in human DLBCL MD901 cells and H3K27ac reduction in MD901 cells transduced with shRNAs against human CREBBP, and stacked bar plot showing the genome-wide distribution of CREBBP ChIPseq peaks in OCI-Ly7 cells. Supplementary Figure S4. GSEA enrichment plots showing correlation of genes with >25% loss of H3K27ac at enhancers in VavP-Bcl2/shCrebbp tumours with ranked expression change between B220+ lymphoma cells from VavP-Bcl2/shCrebbp tumours (n=3) and VavP-Bcl2/GFP tumours (n=3). NES, normalized enrichment score. Supplementary Figure S5. Venn diagram showing the overlap of H3K4me2+H3K4me3-H3K27ac+ (active enhancer) peaks between human tonsilar IgD+ Naïve B cells (NBs) and CD77+ germinal center B cells (GCBs). Supplementary Figure S6. Pathway analysis of down-regulated genes in top 500 differentially expressed genes between murine VavP-Bcl2/shCrebbp tumours and VavP-Bcl2/GFP tumours (left panel), or between CREBBP knockdown and scramble control human DLBLC MD901 cells (right panel). Supplementary Figure S7. Pathway analysis of genes with > 25% reduction of H3K27ac reads at promoters in murine VavP-Bcl2/shCrebbp tumors. Supplementary Figure S8. UCSC read-density tracks of normalized BCL6 (purple) and SMRT (orange) ChIP-seq reads in human tonsilar GCBs, H3K27ac ChIP-seq reads in human tonsilar NBCs (red) and GCBs (blue), and H3K27ac ChIP-seq in control scramble (Scr, green) and CREBBP KD (shCREBBP, turquoise) MD901 cells at the human CIITA and CD74 loci. BCL6 and SMRT peaks determined by MACS2 are indicated by grey bars under the read density track. Supplementary Figure S9. Stacked bar plots showing the frequencies of CREBBP somatic mutations in two cohorts of FL and one cohort of DLBCL primary patient samples. Supplementary Figure S10. The proportions of the Up (up-regulated) and Down (down-regulated) genes in the top 100, 500, and 1000 most differentially expressed genes of the respective cohorts profiled in Figure 3. Supplementary Figure S11. Representative flow cytometry analysis for FAS and GL7 of whole spleens from NS-DAD wild type (wt) or mutant (mut) animals. Supplementary Figure S12. Western blots showing the knockdown efficiency of shRNAs against human HDAC3 in DLBCL cell lines OCI-Ly7 and MD901 120 hr after induction of shRNA expression. The amount of HDAC3 was quantified by using ImageJ, and the ratio of shRNA knockdown samples and the control shLuc sample was indicated below the blots. Supplementary Figure S13. BCL6 and HDAC3 ChIP-qPCR at enhancers of CD74 or HLA-DOA (primer sequences please check Supplementary Table S12) in OCI-Ly1 cells transfected with either non-target siRNA (siNT) or BCL6 siRNA (siBCL6). Supplementary Figure S14. Quantification of HLA-DR measured by flow cytometry in shCREBBP or scramble transduced lymphoma cells MD901 and OCI-Ly18 in a second biological replicate experiment.</p>