| Part I:A study on the prognostic genes of colorectal cancerChapter 1:Discovery of a novel immune gene signature with profound prognostic value in colorectal cancer:a model of cooperativity disorientation created in the process from development to cancerImmune response-related genes play a major role in colorectal carcinogenesis by mediating inflammation or immune-surveillance evasion. Although remarkable progress has been made to investigate the underlying mechanism, the understanding of the complicated carcinogenesis process was enormously hindered by large-scale tumor heterogeneity. Development and carcinogenesis share striking similarities in their cellular behavior and underlying molecular mechanisms. The association between embryonic development and carcinogenesis makes embryonic development a viable reference model for studying cancer thereby circumventing the potentially misleading complexity of tumor heterogeneity.Here we proposed that the immune genes, responsible for intra-immune cooperativity disorientation (defined in this study as disruption of developmental expression correlation patterns during carcinogenesis), probably contain untapped prognostic resource of colorectal cancer. In this study, we determined the mRNA expression profile of 137 human biopsy samples, including samples from different stages of human colonic development, colorectal precancerous progression and colorectal cancer samples, among which 60 were also used to generate miRNA expression profile. We originally established Spearman correlation transition model to quantify the cooperativity disorientation associated with the transition from normal to precancerous to cancer tissue, in conjunction with miRNA-mRNA regulatory network and machine learning algorithm to identify genes with prognostic value. Finally, a 12-gene signature was extracted, whose prognostic value was evaluated using Kaplan-Meier survival analysis in five independent datasets. Using the log-rank test, the 12-gene signature was closely related to overall survival in four datasets (GSE17536, n=177,p=0.0054; GSE17537, n=55,p=0.0039; GSE39582, n=562,p=0.13; GSE39084, n=70,p=0.11), and significantly associated with disease-free survival in four datasets (GSE17536, n=177,p=0.0018; GSE17537, n=55, p=0.016; GSE39582, n=557, p=4.4e-05; GSE14333, n=226, p=0.032). Cox regression analysis confirmed that the 12- gene signature was an independent factor in predicting colorectal cancer patient’s overall survival (hazard ratio:1.759; 95% confidence interval:1.126-2.746; p=0.013], as well as disease-free survival (hazard ratio:2.116; 95% confidence interval:1324-3.380;p=0.002).Chapter 2:Cell cycle related genes up-regulated in human colorectal development predict the overall survival of late-stage colorectal cancer patientsA tumor can be perceived as a special "organ" that undergoes aberrant and poorly regulated organogenesis. Embryonic development and carcinogenesis share striking similarities in their cellular behavior and underlying molecular mechanisms. This intimate association makes embryonic development a viable reference model for studying cancer thereby circumventing the potentially misleading complexity of tumor heterogeneity. Therefore, on the basis of global expression profile, the genes simultaneously activated (up-regulated in terms of expression profile) or suppressed (down-regulated) in both embryonic development and cancer stage, probably contain profound information upon the molecular mechanism of cancer. In this study, the Affymetrix expression profile of 1593 colorectal cancer samples was downloaded from Gene Expression Omnibus. The 1396 differentially expressed probes were robustly obtained using 660 colorectal normal and cancer samples, of which the expression pattern was analyzed in our human colorectal developmental data. All these 1396 probes were classified into 27 distinct patterns based on their expression patterns during the developmental process. By means of gene set enrichment analysis, we collected 393 Ⅴ probes simultaneously up-regulated in both development and carcinogenesis and 207 A probes down-regulated in both. Functional enrichment analysis indicated that Ⅴ probes were significantly related to cell cycle regulation. Notably,28 cell-cycle related probes within Ⅴ probe group were found to be significantly associated with overall survival of Stage Ⅲ/Ⅳ patients (GSE17536 cross validation, n=96, p=5.70e-03; GSE29621, n=36, p=1.70e-03; GSE39084, n=38,p=0.05; GSE39582, n=264,p=0.047; GSE17537, n=36,p=5.90e-03).Chapter 3:Developmental genes significantly afflicted by aberrant promoter methylation and somatic mutation predict overall survival of late-stage colorectal cancerCarcinogenesis is an exceedingly complicated process, which involves multi-level dy sregulations, including genomics (majorly caused by somatic mutation and copy number variation), DNA methylomics, and transcriptomics. Therefore, only looking into one molecular level of cancer is not sufficient to uncover the intricate underlying mechanisms. With the abundant resources of public available data in the Cancer Genome Atlas (TCGA) database, an integrative strategy was conducted to systematically analyze the aberrant patterns of colorectal cancer on the basis of DNA copy number, promoter methylation, somatic mutation and gene expression. In this study, paired samples in each genomic level were retrieved to identify differentially expressed genes with corresponding genetic or epigenetic dy sregulations. Notably, the result of gene ontology enrichment analysis indicated that the differentially expressed genes with corresponding aberrant promoter methylation or somatic mutation were both functionally concentrated upon developmental process, suggesting the intimate association between development and carcinogenesis. Thus, by means of random walk with restart,37 significant development-related genes were retrieved from a priori-knowledge based biological network. In five independent microarray datasets, Kaplan-Meier survival and Cox regression analyses both confirmed that the expression of these genes was significantly associated with overall survival of Stage III/IV colorectal cancer patients.Part Ⅱ:A study on the prognostic genes of lung squamous carcinomaLung squamous carcinoma currently has no effective therapeutic target in clinical management. Therefore, thorough researches regarding the molecular abnormalities during carcinogenesis, especially in precancerous stage, might be helpful in discovering potential biomarkers and promising therapeutic targets. Additionally, embryonic development and carcinogenesis shared many common cellular behaviors and molecular characteristics. Tumor could be perceived as a special organ diverging from normal developmental pathway, suggesting human embryonic development could be a viable reference model to study carcinogenesis. In this study, human lung samples of ten time points, covering from embryonic development to carcinogenesis, were used to construct global expression profile. Differentially expressed genes consistently differentiated in precancerous and cancer samples were collected. Based on network-based greedy searching algorithm using our training cohort (n=69) and three independent testing cohorts, we successfully identified a significant module, containing 22 genes, of which the expression level was significantly correlated with the overall survival of lung squamous carcinoma patients. |
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