A Study On Colorectal Carcinogenesis Associated Gene Expression Profiles

It is reported that embryogenesis and tumorigenesis have many similarities at phenotypic and genetic levels, which provides new directions for investigating the mechanisms of tumorigenesis through embryogenesis. The mRNA expression profiles of three sequent subsets of human colon development tissues and three stages of colorectal tumor tissues were involved in this study, including6early embryonic colon,8middle embryonic colon,12normal adult colorectal mucosa,71low-grade adenoma,33high-grade adenoma and47adenocarcinoma tissues. The gene expression features of colorectal embryogenesis and carcinogenesis were analyzed respectively, and integrative analysis was performed using the data of two processes. The results displayed that genes up-regulated in embryogenesis referred to immune response, antigen presentation, ion transport, cellular homeostasis, apoptosis, etc.; genes down-regulated were involved in DNA replication, chromatin organization, DNA and RNA metabolic process, cell adhesion, cell morphogenesis, regulation of cell development, etc. In colorectal carcinogenesis, the up-regulated genes were associated with transcription regulation, embryonic morphogenesis, extracellular matrix organization, angiogenesis, cell adhesion, cell proliferation, etc.; the down-regulated genes were associated with immune response, activation of immune cells, defense response, inflammatory response, cellular ion homeostasis, etc. Integrative analysis revealed that the gene expression characteristics of colorectal neoplasm were similar to the embryonic colon tissues, and along with colorectal tumor progression, their expression profiles were more approximate to those of the early stage embryonic colon tissues. These results indicate that there is a dynamic connection of mRNA expression between embryogenesis and carcinogenesis. Based on the molecular features described above, two gene clusters with opposite expressing patterns were screened, one was up-regulated during development and down-regulated during carcinogenesis, correlating with immune response and apoptosis; the other was down-regulated during development and up-regulated during carcinogenesis, associating with cell proliferation. In this part, it is concluded that the expression profiles of human colon development and colorectal tumorigenesis are highly similar, and molecular events of colorectal carcinogenesis may be the re-activation or re-inhibition of molecular events related to colon embryogenesis. Therefore, integrative and comparative analysis of colon development and colorectal tumorigenesis will be a promising strategy for colorectal tumor research. Part II:Genes involved in the transition from normal epithelium to intraepithelial neoplasia are associated with colorectal cancer patient survivalWhether the heterogeneity in tumor cell morphology and behavior is the consequence of a progressive accumulation of (epi)genetic alterations or an intrinsic property of cancer-initiating cells established at initiation remains controversial. The hypothesis of biological predetermination in human cancer was proposed many years ago and states that the biological potency of cancer cells is predestinated in the precancerous stage. The present study aimed to investigate whether the aberrant molecular events occurring in initial cancer stages could eventually influence colorectal cancer progression. We analyzed the mRNA and miRNA expression profiles of colorectal normal mucosa, low-grade adenoma, high-grade adenoma, and adenocarcinoma tissues. Compared with the transitions from low-grade to high-grade adenoma to invasive carcinoma, the transition from normal epithelium to low-grade adenoma appeared to be associated with greater changes in the number and expression levels of mRNAs and miRNAs, with a differential expression of2,322mRNAs and71miRNAs detected. Utilizing these early molecular changes, a miRNA-hub network analysis showed that166genes were identified as targets regulated by30miRNAs. Among these genes, a55-gene signature regulated by5miRNAs was shown to be associated with overall survival or disease-free survival in three independent sample sets. Thus, the molecular changes in the transcriptome associated with the transition from normal to intraepithelial neoplasm may influence colorectal cancer progression. Part Ⅲ:A study on colorectal normal mucosa and adenocarcinoma specific conserved gene clustersUtilizing the mRNA expression profiles of colorectal normal mucosa and adenocarcinoma tissues, differentially expressed gene pairs were screened and normal and carcinoma specific conserved gene clusters were constructed, providing new clues to explore the molecular mechanism of colorectal carcinogenesis. The mRNA expression profiles of12normal mucosa,21low-grade adenoma,30high-grade adenoma and25adenocarcinoma tissues were analyzed. Through bioinformatics analysis, the co-expressed gene pairs in each stage of colorectal cancer development were screened and normal mucosa and carcinoma specific co-expression networks (conserved gene clusters) were established. The functions of normal mucosa specific conserved gene clusters were activation of immune cells, complement activation, organ morphogenesis, etc.; the functions of adenocarcinoma specific conserved gene clusters were cell proliferation, cell motility, cell adhesion, etc. We also predicted the potential regulatory genes of the conserved gene clusters. Then, we selected11genes of three clusters (including one normal specific cluster and two carcinoma specific clusters) and8predicted regulatory genes for further validation in initial samples (12normal tissues and22adenocarcomoma tissues) and independent samples (13normal tissues and19adenocarcinoma tissues) by Real time PCR. The results revealed that the positive rates of the19genes differentially expressed between normal and carcinoma were84.21%(16/19) and42.11%(8/19) in initial and independent samples respectively. Additionally, we verified that over-expression of MAFB increased the mRNA expression of the genes in cluster16(RAB31, MYO5A, WIPF1, LCP1) in colorectal cancer cell lines. Therefore, the method of co-expression network construction is feasible, and the colorectal normal mucosa and adenocarcinoma specific conserved gene clusters may contribute to explore the molecular mechanisms of colorectal cancer.