| Differentiation is the demarcation between normality and malignancy of cells. It is not only the diagnostic marker in morphology but also the basement of biologic behaviors. So it is of scientific importance to screen the tumor differentiation-related genes, and to probe into the mechanism of tumor differentiation.However, it has not been reported that gene expression profiling of colorectal cancer (CRC) with different differentiation grades so far. An overall,systematic research of CRC differentiation-related genes is needed.In our study, Affymetrix oligonucleotide microarrays HG-U133 were used to monitor gene expression of about 19308 known genes and 12956 ESTs (altogether 32264) on 9 single samples of CRC with different differentiation grades ( 3 well differentiated, 3 moderately and 3 poorly ) paired normal mucosa tissue ( 9 samples in one pools ). The results were as follows.1. Gene expression profiles of CRC and corresponding normal mucosa tissue were obtained, and the microarray findings were confirmed by real time quantitative reverse transcriptase-polymerase chain reaction ( FQ-PCR ) on MAGE-A3, MMP1, MMP3 and C8orf4.2. 3125 of CRC-related genes & ESTs were obtained.3. 922 of CRC differentiation-related genes & ESTs were chosen. In order to describe their great effect on CRC differentiation, the principle components got by principle component analysis (PCA) were named as "supergene set".4. Utilizing the software of "Gene Ontology", CRC-related genes and CRC differentiation-related genes were functionally classified. Their chromosome locations, cellular components, molecular functions and biological process were known.The functions of CRC-related genes include that binding, catalytic activity, signal transducer activity, transporter activity, enzyme regular activity, obsolote molecular function, structural molecular activity, transcription regular activity and so on.The functions of CRC differentiation-related genes include: binding, catalytic activity, transporter activity, signal transducer activity, transcription regular activity, translation regular activity, structural molecular activity, chaperone activity, enzyme regular activity, apoptosis regulator activity, cell adhesion molecular activity, defense/immunity protein activity and so on.About 32% of CRC-related genes and 36-43% of CRC differentiation-related genes were involved in binding function. Binding is the biggest one in all the function groups.5. Based on the hypothesis that genes with similar functions have similar expression model, 2 ESTs with similar expression profile to the genes involved in binding were supposed to have similar function.6. According to the function analysis of CRC-related genes, the mechanisms of carcinogenesis of CRC may be: the abnormal open( activation ) or shut (inactivation) of the expression of multiple genes brought about the alteration of quality or quantity of encoded proteins, which led to the abnormality of cell signal transducer, degradation of transcription regulator activity, deregulation of proliferation, descent adhesion, evading apoptosis, reinforcement of matrix and collagen hydrolysis, descent defense mechanism and etc.7. According to the function analysis of CRC differentiation-related genes, the genes involved in cell proliferation and motility were absent in well differentiated CRC, the catalytic activity were high in moderatelydifferentiated CRC, and the poorly differentiated CRC had a high energy metabolism activity. It suggests that proliferation and energy metabolism activity may be the important molecular mechanism of the difference of CRC differentiation.The new contributions of our study may be as follows:(1) The new data mining strategy of screening tumor-related genes and differentiation-related genes was designed and confirmed to be effective.(2) The genechip with all genes of human were firstly used in the world to screen the CRC-related genes, and the largest data of CRC-...
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