Additional file 1 of The PD-L1 metabolic interactome intersects with choline metabolism and inflammation
Creators: name: Pacheco-Torres, Jesus
name: Marie-France Penet
name: Mironchik, Yelena
name: Balaji Krishnamachary
name: Bhujwalla, Zaver M.
Publisher: name: figshare
Year: 2021
Subjects: subject: Space Science
subject: Immunology
subject: FOS: Clinical medicine
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Cancer

description: Additional file 1: Supplementary Figure 1. Correlation between the mean expression of Chk-α and PD-L1 in different cancer cell lines when treated with siRNA for 48h corresponding to Figure 1. Plot showing a correlation between mRNA expression level of Chk-α and PD-L1 obtained by RT-PCR of (A) MDA-MB-231, (B) SUM 149, (C) Pa09C and (D) Pa20C cells. Statistical analysis using Pearson’s correlation coefficient showed a significant correlation with P≤0.001 for all except Pa20C cells. Supplementary Figure 2. Representative flow cytometry histograms for MDA-MB-231 cells treated with siRNA corresponding to Figure 2. Representative flow cytometry histograms showing signals from control IgG-APC (blue) and anti-PD-L1-APC (red) antibodies in MDA-MB-231 cells: untreated (A), transfected with 100 nM scrambled siRNA (B), transfected with 100 nM luciferase siRNA (C), transfected with 100 nM Chk-siRNA (D), transfected with 100 nM PD-L1 siRNA (E) and transfected with a mixture of 50 nM PD-L1 and 50 nM Chk-α siRNA (Chk-α + PD-L1) (F). Supplementary Figure 3. Correlation between the expression of Chk-α and PD-L1 in primary tumor tissue among different human cancers corresponding to Figure 7. Individual levels of Chk-α and PD-L1 measured in different tumor types showed a statistically significant correlation (P&lt; 0.001, r=-0.358) according to Spearman's correlation coefficient. Supplementary Figure 4. Comparison between Chk-α and PD-L1 in primary tumors with the highest and lowest values of these genes corresponding to Figure 7. We ranged primary tumors from the TCGA TARGET GTEx database according to their mRNA levels for Chk-α and PD-L1. We selected those samples, irrespective of the tumor type, based on the 10% highest and 10% lowest values for (A) Chk-α and (B) PD-L1. Supplementary Table 1. Mean values of water-soluble metabolite concentrations in MDA-MB-231 cells corresponding to Figure 3. Values were generated from the quantitative analysis of high-resolution 1H MR spectra obtained at 48h from the aqueous phase of MDA-MB-231 cells that were: untreated, transfected with 100 nM luciferase siRNA (Luciferase), transfected with 100 nM Chk-α siRNA (Chk-α), transfected with 100 nM PD-L1 #1 siRNA (PD-L1) and transfected with a mixture of 50 nM PD-L1 and 50 nM Chk-α siRNA (Chk-α + PD-L1). Values represent Mean (mM /cell) ± SEM from 3-6 independent experiments. GPC: glycerophosphocholine, PC: phosphocholine, Cho: choline, GSH: glutathione, GSSG: oxidized glutathione, MTA: S-methyl-5′-thioadenosine. Supplementary Table 2. Mean values of lipid metabolites in MDA-MB-231 cells corresponding to Figure 4. Values were generated from the quantitative analysis of high-resolution 1H MR spectra obtained at 48h from the lipid phase of MDA-MB-231 that were: untreated (control), transfected with 100 nM luciferase siRNA (Luciferase), transfected with 100 nM Chk-α siRNA (Chk-α), transfected with 100 nM PD-L1 #1 siRNA (PD-L1) and transfected with a mixture of 50 nM PD-L1 and 50 nM Chk-α siRNA (Chk-α + PD-L1). Values represent Mean (a.u.) ± SEM obtained from 3-6 independent experiments. Lipids (-CH3): methyl groups of fatty acids, Lipids (-CH2-): methylene groups of fatty acids, OOC-CH2: methylene groups at the α position of the carboxylic function, OOC-CH2-CH2: methylene groups at the β position of the carboxylic function, ARA: arachidonic acid, EPA: eicosapentaenoic acid, PtdEA: phosphatidylethanolamine, PtdCholine: phosphatidylcholine, (CH=CH-CH2-CH=CH)n: diallylic methylene protons, CH=CH-CH2: methylene groups at the α position of a double bond, CH=CH: fatty acid double bonds. Supplementary Table 3. Mean values for Chk-α and PD-L1 expression for 32 different tumor types corresponding to Figure 7. Values were extracted from the TCGA public database and expressed as the Mean ± SEM. The number of tumor samples for each tumor type available in the TCGA data base are also presented. Supplementary Table 4. Correlation coefficients between PD-L1 and Chk-α expression in different tumor types corresponding to Figure 7. Correlation coefficients were calculated used the c-bioportal, and by selecting mRNA Expression Z-scores (RNA Seq V2 RSEM) with a z-score threshold of ±2.0. Statistically significant correlations (p&lt;0.01) are highlighted in bold.