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    • br Significant associations for pre operative protein with

    2020-03-17


    Significant associations for pre-operative protein with clinical char-acteristics were found between loss of heterogeneity of CDH and SMAD4 (p = 0·0005) and between GCNT1 and TNM stage (p = 0·0072).
    3.6. Alteration of serum protein levels before and after surgery
    To check whether protein abundances can be affected by tumour re-section, levels of proteins before operation and one to two weeks after were compared. The univariate analysis with FDR correction for multiple tests showed that 184 of 316 (58·2%) proteins were significantly changed after surgery (88 decreased and 96 increased, Supplementary Table 5). Volcano plots in Fig. 2G-H display the most significantly altered proteins in the comparisons between pre and post groups and between control and post. The biological enrichment analysis by FunRich revealed that the proteins decreased after surgery are predominantly involved in cell adhesion, whereas the proteins increased are tend to be associated with Norfloxacin (Supplementary Fig. 8). Notably, the changes for the protein levels after operation were not consistent in all the patients, but following the same trend in most patients as illustrated for each protein and each patient in Supplementary Fig. 9. We then eval-uated the clinical associations of proteins differentially changed after sur-gery, and found associations between CYR61 with LOH of CDH, between GCNT1 with Lauren classification, and proteins associated with tumour site including ERBB2/3/4, GPNMB, ITGAV, ITGB5, LYPD3, NTRK2/3, SEZ6L, XPNPEP2, and TNFRSF19 (Supplementary Table 6).
    3.7. Optimal proteins combination for distinguishing gastric cancer patients from controls
    Multivariate analysis ENLR was performed to further select promis-ing serum biomarkers and generate a diagnostic model for gastric can-cer. With cross-validation, the optimal α = 0.4 was chosen for penalty proportion for the model according to the lowest misclassification error and the best accuracy (Supplementary Table 7). After ten-fold cross-validation, 27 proteins were retained to have all non-zero coeffi-cients at each cross-validation step (Fig. 3A). By comparing the ROC curves of different combinations of the proteins that ranked from the largest to the smallest absolute regression coefficients, the combination
    A Serum Tissue
    Serum Detectable Detectable
    Tissue
    Undetectable
    Undetectable
    C Tumor tissue vs. Normal tissue
    N
    T
    E Serum_Pre vs. Post vs. Ctrl
    Ctrl
    Pre
    Post
    Serum_Pre vs. Post
    SCF ITGAV
    Pvalues)
    LRRN1
    LEP NTRK2
    SYND1
    LYPD3
    CAV1
    IGF1
    MMP1
    TRANCE CD6
    HMOX1
    adj
    CTSV
    TNFRSF6B
    ICOSLG
    ENRAGE
    (FDR
    OMG
    FGFBP1
    CEACAM5
    ESM1
    TXLNA
    MK
    log2 Fold Change (Pre/Post)  B
    D Tumor tissue vs. Normal tissue
    CPXM1 WISP1
    MCP3
    SPARC ESM1
    VEGFD
    CCL4CXCL6
    IL8 OSM
    SULT2A1
    h
    CXCL1MCP2 IL6 IL1 alpha
    DNER
    MMP1
    P
    CFC1
    ERBB4
    TNFRSF6B
    MICA/B
    OPG
    MSLN
    DNAJB1
    Serum_Pre vs. Ctrl
    MMP1
    CA9 MCP3
    P
    MSLN CEACAM5
    AR
    ENRAGE
    DCTN2 IL8
    log2 Fold Change (Pre/Ctrl)
    H Serum_Ctrl vs. Post
    NTRK2
    ENRAGE MMP1
    NTRK3
    SCF ITGAV
    SYND1
    DNER
    ITGA1
    IL7 MCP3
    adj
    SIGLEC10
    DNAJB1
    TRANCE CTSV
    CXCL1 CCL20
    MK
    LRRN1
    IGF1
    ICOSLG
    AR
    log2 Fold Change (Post/Ctrl)
    Table 2
    Clinical significance of proteins expressed in gastric cancer tumour tissue.
    Variables r> Protein Padj
    MSI status
    BOC 0·0403