Additional file 8 of Mapping three-dimensional intratumor proteomic heterogeneity in uterine serous carcinoma by multiregion microsampling

Additional file 8: Table S1. Clinical features and manual pathology assessment of tumor purity throughout the depths of USC patient specimen blocks. Representative H&E stained tissue sections on glass slides were examined at ~100 µm intervals by a board-certified pathologist for evaluation of the relative contributions (as percentages) of tumor cellularity, stroma, necrosis, normal ovarian epithelium, lymphocytes, and polymorphonuclear leukocytes (PMN) to the overall tissue composition. Multiple images per level/case were reviewed; the median estimates of tumor and stroma cellularity are reported with corresponding coefficient of variation (%CV) reported in parentheses. Abbreviations: NACT= neoadjuvant chemotherapy; NOS= not otherwise specified. Table S2. Depiction of study cohort. Numerical values indicate the number of LMD tissue sections that were used for each collection. Greyed boxes represent samples that were not collected or did not have sufficient yield of the target analyte for analysis. Table S3. Global protein matrix. Log2 transformed fold-change abundances of 6503 proteins co-quantified across all samples (n=118). Table S4. Transcriptome matrix for case 343VY. Log2-transformed normalized abundances of 15,558 RNA transcripts measured in case 343VY calculated relative to the average RPM abundance quantified across all samples for a given transcript. Table S5. Log2-transformed target-wise median centered RPPA abundances of protein and phosphoprotein targets in ET, ES, and BT samples. Table S6. Cell type enrichment scores using transcriptomic data for case 343VY in xCell ( http://xcell.ucsf.edu/ , [21]). Table S7. Cell type enrichment scores using proteomic data in xCell ( http://xcell.ucsf.edu/ , [21]). Table S8. ssGSEA scores calculated from “tumor”, “stroma”, and “immune” classifiers. Table S9. Median absolute deviation (MAD) of LMD enriched samples expressing or lacking signal peptide sequences and extracellular classification. P-values indicate the reliability of the presence or absence of a signal peptide or extracellular classification within the indicated LMD enriched tissue across all levels/case. Table S10. Spearman correlations for co-quantified proteins and transcripts from case 343VY. Spearman correlations were calculated using Log2 transformed fold-change abundances of 6,019 imputed proteins that were co-measured as transcripts. Table S11. Spearman correlations between samples using proteins co-quantified by MS and RPPA. Table S12. Spearman correlations for proteins co-quantified by MS and RPPA. Table S13. Pairwise Spearman correlations within and between ET and ES samples using proteins with MAD>1 for construction of patient-specific dendrograms. Table S14. Pairwise Spearman correlations between BT harvests using proteomic abundances. Table S15. LogFC values of proteins measured in HGSOC specimens which were commonly differentially expressed (limma adj. p<0.05) in ET and ES from USC specimens. LogFC protein abundances from Hunt et al Table S7 [13] which displayed the same pattern of expression and passed limma adj. p<0.05 across all patients were prioritized for comparative analysis with LMD enriched samples from USC specimens. The median LogFC values for 313 proteins co-altered from HGSOC samples, which were used as input for Ingenuity Pathway Analysis (IPA). Proteins reported in this table correspond to the HGSOC LogFC values for proteins in the center panel of the venn diagram in Fig. 6. Table S16. LogFC values of proteins measured in USC specimens which were commonly differentially expressed (limma adj. p<0.05) in ET and ES from HGSOC specimens. LogFC protein abundances from USC LMD enriched samples which displayed the same pattern of expression across all patients were prioritized for comparative analysis with LMD enriched samples from HGSOC specimens. The median LogFC values for 313 proteins co-altered from USC samples, which were used as input for Ingenuity Pathway Analysis (IPA). Proteins reported in this table correspond to the USC LogFC values for proteins in the center panel of the venn diagram in Fig. 6. Table S17. LogFC values of proteins measured in HGSOC specimens which were uniquely differentially expressed (limma adj. p<0.05) in ET and ES, which were not co-altered in LMD enriched samples from USC specimens. The 483 proteins reported in this table correspond to the HGSOC only LogFC values for proteins in the left panel of the venn diagram in Fig. 6. Table S18. LogFC values of proteins measured in USC specimens which were uniquely differentially expressed (limma adj. p<0.05) in ET and ES, which were not co-altered in LMD enriched samples from HGSOC specimens. The 142 proteins reported in this table correspond to the USC only LogFC values for proteins in the right panel of the venn diagram in Fig. 6. Table S19. Drug targets and canonical pathways identified by Ingenuity Pathway Analysis (IPA) significantly altered in ET and ES from USC and/or HGSOC specimens. Targets and pathways designated as “HGSOC only” correspond to the those identified using the 483 uniquely differentially expressed proteins between ET and ES from Additional file 8: Table S16 (Fig. 6, left panel of venn diagram). Targets and pathways designated as “USC only” correspond to the those identified using the 142 uniquely differentially expressed between ET and ES from Additional file 8: Table S17 (Fig. 6, right panel of venn diagram). Targets and pathways designated as “Overlap” correspond to those identified when using the HGSOC and USC (as specified) LogFC values of the 313 proteins in Additional file 8: Tables S14 and S15, respectively, as input.