Supplementary Data - Tables S1-S17 from A Unique Morphological Phenotype in Chemoresistant Triple-Negative Breast Cancer Reveals Metabolic Reprogramming and PLIN4 Expression as a Molecular Vulnerability

Emma Fowler,Urszula Krzemien,André Robidoux,Catherine Chabot,Luca Cavallone,Catalin Mihalcioiu,Stephen D Hursting,Stéphanie Légaré,Christoph H Borchers,Aparna Ramanathan,Marguerite Buchanan,Marie-Christine Guilbert,Josiane Lafleur,Sheida Nabavi,Amine Saad,Ewa Przybytkowski,Olga Aleynikova,Banujan Balachandran,Eric Bareke,Sylvia Josephy,Mark Basik,Horace Uri Saragovi,René P Zahedi,Naciba Benlimame,Elizabeth A Marcus,Cathy Lan,Isabelle Sirois,Michelle Scriver,Jacek Majewski,Josée-Anne Roy,Cristiano Ferrario,Vincent Richard ,Ciara H O’flanagan ,Moulay A Alaoui‐Jamali ,Peter J Tonellato ,Adriana Aguilar‐Mahecha ,Viet T Vu

doi:10.1158/1541-7786.22515957.v1

Abstract

<p>Table S1: List of regions of genes with increased CNV (>= 0.5) and gene expression (>= 0.5) in DOXO-R cells compared to parental cells Table S2: List of all fold change and pvalue of DOXO-R C1 and C8 (vs parental cells) from gene expression analysis. Table S3. GSEA using the C5 module for the 1852 genes with gene expression fold change > 1.5 (pval < 0.05) in DOXO-R C1 and C8 Table S4. GSEA using the C5 module for the 407 genes with gene expression fold change > 1.5 (pval < 0.05) and CNV change > 0.5 Table S5: Mean LOG2FC of genes commonly up-regulated in C1 and C8 Table S6: Proteins that are significantly upregulated according to the following criteria. (i) only present in one or two of the Dox resistant cell lines (**) with at least 3 and 2 unique peptides, respectively. (ii) At least 1.5-fold upregulated in both cell lines with a maximum relative standard deviation (RSD) of 31% across control replicates and 25% RSD across resistant cell line replicates. Table S7: GSEA using the C5 module for the 98 overexpressed proteins in DOXO-R vs parental cells Table S8: mRNA fold change (POST vs PRE NAC) for 9 chemoresistant TNBC patients. Table S9: GSEA using the C5 module for NEO2 up regulated genes > 2.5 FC. The complete list of genes are listed below the GSEA analysis. Table S10: GSEA using the C5 module for NEO24 up regulated genes > 2.5 FC. The complete list of genes are listed below the GSEA analysis. Table S11: GSEA using the C5 module for NEO25 up regulated genes > 2.5 FC. The complete list of genes are listed below the GSEA analysis. Table S12: GSEA using the C5 module for NEO27 up regulated genes > 2.5 FC. The complete list of genes are listed below the GSEA analysis. Table S13: GSEA using the C5 module for NEO28 up regulated genes > 2.5 FC. The complete list of genes are listed below the GSEA analysis. Table S14: GSEA using the C5 module for NEO30 up regulated genes > 2.5 FC. The complete list of genes are listed below the GSEA analysis. Table S15: GSEA using the C5 module for NEO31 up regulated genes > 2.5 FC. The complete list of genes are listed below the GSEA analysis. Table S16: GSEA using the C5 module for NEO35 up regulated genes > 2.5 FC. The complete list of genes are listed below the GSEA analysis. Table S17: GSEA using the C5 module for NEO44 up regulated genes > 2.5 FC. The complete list of genes are listed below the GSEA analysis.</p>

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