Supplementary Figures from Peritoneal Microenvironment Promotes Appendiceal Adenocarcinoma Growth: A Multi-omics Approach Using Patient-Derived Xenografts
Authors: Pattalachinti Vinay K. , Ito Ichiaki , Chowdhury Saikat , Yousef Abdelrahman , Gu Yue , Gunes Betul Beyza , Salle Emma R. , Taggart Melissa W. , Fournier Keith , Fowlkes Natalie W. , Shen John Paul 
Published: April 2024

<p>Figure S1: Individual chromogenic IHC figures for CDX2, Vimentin, and KU80 used to create the merged images shown in Figure 1a.
Figure S2: Plots comparing tumor purity, which is the percent of total reads from a sample that were assigned to human reads, between models and implant sites.
Figure S3: Volcano plot displaying differentially expressed genes (DEGs) from TM00351 peritoneal tumor microenvironment (TME) vs. TM00351 flank TME. Points were colored based on overlap with differentially expressed genes (DEGs) from comparing normal human visceral omentum against human subcutaneous adipose tissues. PDX unique DEGs are genes that were DEGs in the PDX TME comparison but were not differentially expressed in the human tissue comparison.
Figure S4: Volcano plot displaying differentially expressed genes (DEGs) from PMCA-3 peritoneal tumor microenvironment (TME) vs. PMCA-3 flank TME. Points were colored based on overlap with differentially expressed genes (DEGs) from comparing normal human visceral omentum against human subcutaneous adipose tissues. PDX unique DEGs are genes that were DEGs in the PDX TME comparison but were not differentially expressed in the human tissue comparison.
Figure S5: Volcano plot displaying differentially expressed genes (DEGs) from AAP16 peritoneal tumor microenvironment (TME) vs. AAP16 flank TME. Points were colored based on overlap with differentially expressed genes (DEGs) from comparing normal human visceral omentum against human subcutaneous adipose tissues. PDX unique DEGs are genes that were DEGs in the PDX TME comparison but were not differentially expressed in the human tissue comparison.
Figure S6: Venn diagram showing overlap of high effect size differentially expressed genes (DEGs) (log2foldchange≥1 and padj≤0.05) that were relatively upregulated in the PDX peritoneal TME (vs. flank TME) and were relatively upregulated in the human visceral omentum (vs. human subcutaneous adipose tissue).
Figure S7: TME Gene Set Enrichment analysis (GSEA) results for either all three models combined (top row) or each model separately (bottom three rows).
Figure S8: Heatmaps using ward.D clustering on tumor transcriptome with the top 500 highest variance genes (left), tumor transcriptome with only differentially expressed genes (middle), and tumor microenvironment transcriptome with the top 500 highest variance genes (right). Z-transformed across rows. Each row represents a single gene.
Figure S9: PCA plot using the human tumor transcriptomes subset to only the 223 differentially expressed genes identified by comparing expression in the peritoneal implant site to the flank implant site.
Figure S10: Chromogenic Immunohistochemistry for KI67 (brown) split by implanted model (columns) and implant site (rows) alongside the same sample with H&E staining.
Figure S11: Normalized counts for select genes specified in the leading-edge analysis that are relatively enriched by the peritoneal microenvironment split between genes upregulated in the goblet cell gene set (top) and the cell division gene sets (bottom).
Figure S12: Normalized counts for select genes specified in the leading-edge analysis that are relatively enriched by the flank microenvironment.
Figure S13: Volcano plots displaying differentially expressed genes (DEGs) from comparing intraperitoneal (IP) PDX tumor transcriptomes from TM00351 compared to flank PDX tumor transcriptomes from TM00351.
Figure S14: Volcano plots displaying differentially expressed genes (DEGs) from comparing intraperitoneal (IP) PDX tumor transcriptomes from PMCA-3 compared to flank PDX tumor transcriptomes from PMCA-3.
Figure S15: Volcano plots displaying differentially expressed genes (DEGs) from comparing intraperitoneal (IP) PDX tumor transcriptomes from PMCA-3 compared to flank PDX tumor transcriptomes from PMCA-3.
Figure S16: Gene Set Enrichment Analysis (GSEA) conducted using differentially expressed genes (DEGs) from comparing TM00351 PDXs.
Figure S17: Gene Set Enrichment Analysis (GSEA) conducted using differentially expressed genes (DEGs) from comparing PMCA-3 PDXs.
Figure S18: Gene Set Enrichment Analysis (GSEA) conducted using differentially expressed genes (DEGs) from comparing AAP16 PDXs.
Figure S19: Individual reverse phase protein array (RPPA) data for all of the identified proteins, z-transformed across rows separately for each model.</p>