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Breast tumors educate the proteome of stromal tissue in an individualized but coordinated manner

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Sci. Signal.  08 Aug 2017:
Vol. 10, Issue 491, eaam8065
DOI: 10.1126/scisignal.aam8065
  • Fig. 1 Cross-species proteomic profiling finds that the proteome of breast cancer PDXs share common protein abundance changes in both the tumor and microenvironment across biological replicates.

    (A) Number of genes, proteins, and peptides identified from species- and gene-unique peptide sequences. (B) Box plot presentation of protein abundance correlation for all seven PDXs (n = 3) within biological replicates of the same PDX (intra-PDX) compared to other PDXs (inter-PDX) for the tumor (human) and naïve microenvironment (mouse). The P value of the correlation differences between intra- and inter-PDX mouse proteins was 2.7 × 10−7. (C) Clustered heatmaps of differentially regulated human and mouse proteins. Each column represents a biological replicate of each PDX. Male mice used for six of the basal subtype PDX samples are denoted (hash). Values are median normalized by column and log2-transformed. (D) PCA of differentially regulated human and mouse proteins, with each point representing one of three biological replicates for each PDX.

  • Fig. 2 Individual breast PDXs have unique microenvironmental protein signatures.

    (A) Unbiased MSigDB annotation of proteins (by gene symbol) found within each stromal cluster. (B) Bar plots of relative protein abundance for specific molecular signatures including the ECM, complement system (Complement sys.), ER biology, and TAMs. Each PDX has a unique signature consisting of multiple proteins within each category. Error bars are the SD of biological replicates (n = 3). (C) Differential patterns of mouse protein signatures were observed between individual tumors. Gene sets annotated in (A) were used to compare with the baseline using a Student’s t test for each combination of gene set and tumor. The intensity of color key is proportional to the magnitude of −log10 adjusted P value (Benjamini-Hochberg method). Color choices are assigned according to the directionality of deviation from baseline protein abundance (red, up; blue, down). Three biological replicates were analyzed for each PDX.

  • Fig. 3 Stromal proteomic signatures separate patient breast tumors by stage and subtype.

    (A) Spearman’s correlation coefficients for both the mRNA (n = 1095, TCGA) and protein (n = 77, CPTAC) data sets (by gene symbol) of stromal clusters IV to VI. Because the complement system is regulated at the protein level (38), only protein results are shown for cluster IV. (B) P values for the correlation matrices determined using Monte Carlo simulation by sampling 10,000 randomized sets of equal size to the test clusters and ranking the sums of the Spearman’s correlation coefficients. (C and D) Box plot of CPTAC proteomics data (37) for proteins in clusters IV and VI by intrinsic subtype (C) and tumor stage (D) (n = 77). Error bars are SEM. P value is determined by Student’s t test.

  • Fig. 4 Tumor proteins that are highly correlated with stromal protein clusters.

    (A) Unbiased MSigDB annotation of proteins found within each stromal (mouse) cluster and assignment to Hanahan and Weinberg’s Hallmarks of cancer (n = 21 PDX tumors) (41). FDR was calculated using default parameters in GSEA. (B) Correlation of proteins of individual tumor (human) proteins to stromal (mouse) protein clusters (n = 21 PDX tumors). Numbers of significant (Benjamini-Hochberg adjusted P < 0.05) positive (red) and negative (blue) correlations between human proteins and mouse protein clusters are indicated on the x axis. Human proteins are displayed by the genome coordinates of their genes based on University of California, Santa Cruz hg19 annotation.

  • Table 1 Tumor proteins most correlated with stromal proteomic signatures.

    Human proteins (by gene symbol) most correlated to specific stromal protein signatures. The median Spearman’s correlation coefficients (ρ) are highlighted as red (positive) or blue (negative) in breast PDX tumors (n = 21).

    Stromal clusterHuman
    protein
    No. of correlated
    stromal proteins
    (% proteins in cluster)
    ρStromal clusterHuman
    protein
    No. of correlated
    stromal proteins
    (% proteins in cluster)
    ρ
    IZNF6389 (41)0.71IVCUTA12 (44)0.78
    CS7 (32)0.71ABCF110 (37)0.77
    PIP4K2C7 (32)0.73PXDN9 (33)0.80
    ZNF3266 (27)0.74APOA1BP9 (33)0.76
    MDC16 (27)0.73DSG29 (33)0.75
    ALDH4A16 (27)0.74IGSF89 (33)0.75
    HSPA1B6 (27)0.78PSIP19 (33)0.74
    SF3B26 (27)0.69ADK12 (44)−0.73
    CFL27 (32)−0.70GSR11 (41)−0.74
    LGALS3BP7 (32)−0.73PRDX311 (41)−0.73
    ITGA26 (27)−0.75GSDMD10 (37)−0.75
    LRPAP16 (27)−0.72LACTB29 (33)−0.81
    DEGS16 (27)−0.76CD639 (33)−0.71
    RCN16 (27)−0.75IVD8 (30)−0.80
    RNH16 (27)−0.71PNPO8 (30)−0.73
    ARFGEF18 (30)−0.71
    IIPDCD410 (63)0.76REEP58 (30)−0.78
    ANP32A8 (50)0.74RMDN18 (30)−0.76
    GGCT8 (50)0.78SLC25A38 (30)−0.75
    ERMP17 (44)0.79
    HMGN17 (44)0.73VMAP1B10 (29)0.73
    ST137 (44)0.73PEA159 (26)0.73
    NRD19 (56)−0.72GBE19 (26)0.72
    SEPT118 (50)−0.74USP9X9 (26)0.71
    HDLBP7 (44)−0.74ARL28 (24)0.73
    PLOD37 (44)−0.75CFL18 (24)0.72
    HOOK37 (44)−0.74HINT18 (24)0.71
    FTH17 (44)−0.77SERPINH18 (24)0.74
    CYB5B7 (44)−0.78TRIM289 (26)−0.78
    HN17 (44)−0.72C21ORF338 (24)−0.76
    ESRP18 (24)−0.74
    IIIARHGDIB4 (20)0.73PEBP17 (21)−0.75
    IARS23 (15)0.73RAD507 (21)−0.72
    ECI13 (15)0.73
    MRI13 (15)0.76VIMVP8 (31)0.75
    SORD3 (15)0.69ENO38 (31)0.73
    PSMD53 (15)0.69PFKP8 (27)0.72
    SLC9A3R23 (15)0.82HLA.A7 (27)0.72
    STARD103 (15)0.69PSMB87 (27)0.78
    TPD523 (15)0.75MSRA6 (23)0.71
    ATP1B34 (20)−0.71TSTD110 (38)−0.77
    LRRC594 (20)−0.72DHCR710 (38)−0.74
    TRIP103 (15)−0.71APOA1BP9 (35)−0.78
    PFN13 (15)−0.69PEX198 (31)−0.75
    FLNA3 (15)−0.71HYOU17 (27)−0.72
    DPYSL33 (15)−0.73
    TPD52L23 (15)−0.72
    AHNAK23 (15)−0.72
    NXF13 (15)−0.70

Supplementary Materials

  • www.sciencesignaling.org/cgi/content/full/10/491/eaam8065/DC1

    Fig. S1. Framework to study the tumor-intrinsic biology of breast cancer PDXs.

    Fig. S2. Data processing workflow of finding species- and gene-unique PSMs.

    Fig. S3. Correlation (R2) plot of protein abundance between all biological and process replicates in the data set pre-ANOVA filtering.

    Fig. S4. PCA of ANOVA-filtered proteins labeled by mouse gender.

    Fig. S5. mRNA and protein abundance of the stromal proteomic signatures in individual TCGA tumors.

    Fig. S6. TMT10 pooling and data acquisition.

    Fig. S7. Comparison of TMT10 global reference pools A and B.

    Table S1. Metastatic information and passage number of PDX in each biological replicate.

    Table S2. TMT10 labeling schematic for all samples analyzed.

    Table S3. PDX protein abundance.

    Table S4. List of all proteins significantly correlated with each stromal cluster.

    Data file S1. List of all proteins and correlation values (r) in each stromal cluster.

  • Supplementary Materials for:

    Breast tumors educate the proteome of stromal tissue in an individualized but coordinated manner

    Xuya Wang, Arshag D. Mooradian, Petra Erdmann-Gilmore, Qiang Zhang, Rosa Viner, Sherri R. Davies, Kuan-lin Huang, Ryan Bomgarden, Brian A. Van Tine, Jieya Shao, Li Ding, Shunqiang Li, Matthew J. Ellis, John C. Rogers, R. Reid Townsend, David Fenyö,* Jason M. Held*

    *Corresponding author. Email: david{at}fenyolab.org (D.F.); jheld{at}wustl.edu (J.M.H.)

    This PDF file includes:

    • Fig. S1. Framework to study the tumor-intrinsic biology of breast cancer PDXs.
    • Fig. S2. Data processing workflow of finding species- and gene-unique PSMs.
    • Fig. S3. Correlation (R2) plot of protein abundance between all biological and process replicates in the data set pre-ANOVA filtering.
    • Fig. S4. PCA of ANOVA-filtered proteins labeled by mouse gender.
    • Fig. S5. mRNA and protein abundance of the stromal proteomic signatures in individual TCGA tumors.
    • Fig. S6. TMT10 pooling and data acquisition.
    • Fig. S7. Comparison of TMT10 global reference pools A and B.
    • Table S1. Metastatic information and passage number of PDX in each biological replicate.
    • Table S2. TMT10 labeling schematic for all samples analyzed.
    • Legends for tables S3 and S4
    • Legend for data file S1

    [Download PDF]

    Technical Details

    Format: Adobe Acrobat PDF

    Size: 2.13 MB

    Other Supplementary Material for this manuscript includes the following:

    • Table S3 (Microsoft Excel format). PDX protein abundance.
    • Table S4 (Microsoft Excel format). List of all proteins significantly correlated to each stromal cluster.
    • Data file S1 (.txt fomat). List of all proteins and correlation values (r) in each stromal cluster.

    [Download Tables S3 and S4]

    [Download Data file S1]


    Citation: X. Wang, A. D. Mooradian, P. Erdmann-Gilmore, Q. Zhang, R. Viner, S. R. Davies, K.-i. Huang, R. Bomgarden, B. A. Van Tine, J. Shao, L. Ding, S. Li, M. J. Ellis, J. C. Rogers, R. R. Townsend, D. Fenyö, J. M. Held, Breast tumors educate the proteome of stromal tissue in an individualized but coordinated manner. Sci. Signal. 10, eaam8065 (2017).

    © 2017 American Association for the Advancement of Science