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  • CDK GINS PHF A and ERBB genes

    2020-08-28

    # CDK1, GINS2, PHF5 A and ERBB2 Clozapine-N-oxide are associated with poor disease free survival. So these genes are associated exclusively with survival.
    Fig. 2. Interactions between concordant genes-.
    A. Protein-protein interactions of selected markers in The Search Tool for the Retrieval of Interacting Genes/Proteins database network identified 2 major clusters. The bigger cluster involves CDK1, GINS, CCNB1 and CCNB2. The second major cluster included VEGFA, ERBB2, STAT3, CDH1, CTNNB1, CTNND1, KDR. B. The gene interaction networks between 54 genes in Gene mania and Cytoscape identified CDK1, VEGFA, STAT3, ERBB2, AURKA, CDH1, MELK and UBE2C as the major nodes of interactions (indicated in yellow). These genes interact with more than 20 genes.
    Fig. 3. Disease-free survival (DFS) analysis of markers in The Cancer Genome Atlas.
    S. Mohanta et al.
    Table 4
    Co-relation of markers alterations with clinical and pathological parameters.
    OS
    T Stage CDK1
    NS
    HOXA1
    NS
    NS
    NQO1
    NS
    NS
    NS
    RIT1
    NS
    NS
    NS
    FKBP4
    NS
    NS
    NS
    GINS2
    NS
    NA
    PHF5A
    ERBB2
    NS
    NS
    NS
    Markers
    N0 p values
    DFS
    OS
    N Stage
    CDK1
    NS
    NS
    HOXA1
    NS
    NS
    NS
    NQO1
    NS
    NS
    NS
    RIT1
    NS
    NS
    NS
    FKBP4
    NS
    GINS2
    NS
    NS
    PHF5A
    ERBB2
    NS
    NS
    NS
    Markers Recurrent Disease free p values DFS
    OS
    Prognosis CDK1
    NS
    HOXA1
    NQO1
    RIT1
    FKBP4
    GINS2
    NS
    NS
    PHF5A
    ERBB2
    OS
    packs
    packs
    Smoking
    CDK1
    NS
    NS Habit
    HOXA1
    NS
    NS
    NQO1
    NS
    NS
    NS
    RIT1
    FKBP4
    NS
    NS
    NS
    GINS2
    NS
    NS
    NS
    PHF5A
    NS
    NS
    ERBB2
    NS
    NS
    Markers Positive Negative p values DFS
    OS
    Margin Status CDK1 8%
    NS
    NS
    NS
    NS
    NS
    RIT1
    NS
    NS
    NS
    NS
    NS
    NS
    NS
    NS
    NS
    NS
    NS
    Markers Positive Negative p values DFS OS
    Angio lymphatic
    CDK1
    NS
    NS NS
    NQO1
    NS
    NS NS
    RIT1
    NS
    NS NS
    GINS2
    NS
    NS NS
    NS NS
    NS
    NS NS
    Markers Positive Negative p values DFS
    OS
    Extra Capsular
    CDK1
    HOXA1
    NS
    NS
    NQO1
    NS
    NS
    RIT1
    NS
    NS
    FKBP4
    GINS2
    NS
    NS
    PHF5A
    NS
    NS
    ERBB2
    NS
    Table 4 (continued)
    Markers Positive Negative p values DFS OS
    DFS = Disease free survival, OS = Overall survival, NS = Not Significant.
    3.4. Validation of markers in the patient cohort
    Patients diagnosed with primary oral cancer during the period 2010–2015 were screened (n = 100) and based on availability of tis-sues Clozapine-N-oxide from treatment naïve surgical samples and a minimum of 2 years follow up, 28 patients were selected for a pilot validation. Among the patient cohort, 71% (20/28) patients were with risk habits, 75% (21/
    Table 5
    Details of Oral Squamous Cell Carcinoma patient Cohort.
    Variables Outcome Numbers (%) Variables Outcome Numbers (%)
    Status Survived 16 (57)
    3.4.2. Gene expression of selected markers
    A subset of the 12 marker panel (HOXA1, RIT1, FKBP4, NQO1, CDK1, GINS2, ERBB2, UBE2C) that correlated with both disease free/ overall survival and with high fold difference in mRNA expression in The Cancer Genome Atlas analysis were selected for validation in the patient samples. All the primers (Supplementary Table-7) except GINS2 and HOXA1, used for validation showed an efficiency ranging from 1.9 to 2.1 with the percentage efficiency being 93% to 110%. Ribosomal Protein Lateral Stalk Subunit P0 and 18SrRNA were identified as the most stable reference genes; validation of the selected genes was carried out with the relative quantification method using the geometric mean of the two reference genes (normalization) and with the median ex-pression of non-recurrent patients as the baseline.
    The expression profiling of RIT1, FKBP4, NQO1, ERBB2, UBE2C and CDK1 was carried out in recurrent as well as non-recurrent patient cohort. Comparison of the median gene expression indicated an in-creased expression of CDK1 (1.97 vs 0.8), NQO1 (1.1 vs 0.7) in the recurrent cohort vs non-recurrent cohort and in the patients with poor overall survival; NQO1 (1.2 vs 0.7), CDK1 (2.25 vs 0.74). The other genes did not show any difference in the expression profile (Fig. 5A, B). Receiver Operating Curve analysis also indicated these markers as the best markers for recurrence and survival (Area under curve: 0.6), with > 70% sensitivity and > 60% specificity (Table 6). Further ana-lysis was carried out by classifying the patients into markerhigh and markerlow based on cut-off values for each marker. Assessment of the percentage of expression in the sub cohorts indicated that while all the markers showed high expression in the recurrent cohort, RIT1 (1/11; 9% vs 6/17; 35%), NQO1 (3/11; 27% vs 9/17; 52%) and CDK1 (4/11; 36% vs 12/17; 71%) were expressed in the highest percentage of the patients in this cohort. In the deceased group, along with these markers, FKBP4 (2/11; 18% vs 5/17; 29%) also showed a difference in expres-sion (Fig. 5 C, D).