A five-gene signature is associated with tumor progression and poor prognosis in colorectal cancer
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ABSTRACT: We developed an experimentally derived molecular signature from mouse tumor models that is closely associated with survival of colorectal cancer (CRC) patients. We isolated single cell-derived progenies (SCPs) from the SW480 CRC cell line and compared their metastatic potential in an orthotopic implantation model of murine CRC. We compared the differences in the gene expression profiles of a high metastatic variant SCP51, a low metastatic variant SCP58 and their parent SW480/EGFP.
Project description:Gene expression profiling has been widely used to screen for metastasis-associated genes by comparing the difference in paired primary and metastatic colorectal carcinomas, orthotopic implantation mouse model or cells with different metastatic potential in the field of CRC research In our study, we observed that the genes differentially expressed in M5 relative to its parent SW480 cell line Here we used the SW480, a human CRC cell line, as a model system. In vivo variant lines with increasing metastatic capacity were selected in a metastatic orthotopic model of human CRC. A subpopulation named as M5 with enhanced metastatic abilities to liver was isolated by in vivo selection of SW480 cells. We identified genes associated with tumor metastasis by comparing the difference between high metastatic subclone and its parent cells.
Project description:Two isogenic human colorectal cancer cell lines (primary SW480 cell line and its lymph node metastatic variant SW620 cell line),as an in vitro metastatic model. We have demonstrated that SW620 cell line possesses high metastasis potential and SW480 cell linepossesses low metastatic potential. We want to compare the whole cell microRNAs profiles of two isogenic colorectal cancer cell lines (SW480 and SW620 cell line), to gain an insight into the molecular events of colon cancer metastasis.
Project description:Epitranscriptomic reader, writer and eraser (RWE) proteins are involved in the recognition, installation, and removal, respectively, of chemical modifications in RNA, and aberrant expressions of some of these proteins were found to be associated with cancer initiation and progression. Here, we our recently established parallel-reaction monitoring (PRM)-based targeted proteomic method, in conjunction with stable isotope labelling by amino acids in cell culture (SILAC), to investigate the differential expression of epitranscriptomic RWE proteins in a matched pair of primary/metastatic colorectal cancer (CRC) cells (i.e., SW480/SW620) derived from the same patient. We were able to detect 113 non-redundant epitranscriptomic RWE proteins in these two lines of cells. We found that 48 and 5 proteins were respectively up- and down-regulated by at least 1.5-fold in SW620 over SW480 cells. Particularly, NAT10, HNRNPC, and DKC1 were markedly up-regulated, and their potential roles in driving CRC metastasis were supported by recent studies. Interrogation of the Clinical Proteomic Tumor Analysis Consortium (CPTAC) data revealed that the elevated expressions of these and other RWE proteins are also accompanied with CRC initiation, suggesting the roles of these proteins in both the initiation and metastatic transformation of CRC. It can be envisaged that the established PRM method can be further utilized to examine the roles of epitranscriptomic RWE proteins in the metastatic transformations of other types of cancer.
Project description:The transcription factor Snail is known as an EMT regulator to promote cancer metastasis. Identification Snail-regulated miRNAs helps to uncover mechanisms governing CRC metastasis The stable SW480-vector and Snail-expressing cells were established for miRNA microarray analysis.
Project description:Understanding cancer metastasis at the proteoform level is crucial for discovering new protein biomarkers for cancer diagnosis and drug development. Proteins are the primary effectors of function in biology and proteoforms from the same gene can have drastically different biological functions. Here, we present the first qualitative and quantitative top-down proteomics (TDP) study of a pair of isogenic human metastatic and non-metastatic colorectal cancer (CRC) cell lines (SW480 and SW620). This study pursues a global view of human CRC proteome before and after metastasis in a proteoform-specific manner. We identified 23,319 proteoforms of 2,297 genes from the CRC cell lines using capillary zone electrophoresis-tandem mass spectrometry (CZE-MS/MS), representing nearly one order of magnitude improvement in the number of proteoform identifications from human cell lines compared to literature data. We identified 111 proteoforms containing single amino acid variants (SAAVs) using a proteogenomic approach and revealed drastic differences between the metastatic and non-metastatic cell lines regarding SAAVs profiles. Quantitative TDP analysis unveiled statistically significant differences in proteoform abundance between the SW480 and SW620 cell lines on a proteome scale for the first time. Ingenuity Pathway Analysis (IPA) disclosed that many differentially expressed genes at the proteoform level had diversified functions and were closely related to cancer. Our study represents a milestone in TDP towards the definition of human proteome in a proteoform-specific manner, which will transform basic and translational biomedical research.
Project description:Two colon cancer cell lines, SW480 and SW620, were originated from the same patient. The SW480 cell line was derived from a primary lesion, and the SW620 cell line was cultured from a lymph node metastasis with no intervening chemotherapy at a later time. Since these two cell lines are from a single person, it is likely that differences between the two cell lines represent the changes when cancer cells acquire metastatic potential. Thus, this system represents a perfect model for the study of metastatic mechanism. To investigate cancer metastasis associated miRNAs, we detected the miRNA profiles in these two cell lines.
Project description:Investigation of whole genome gene expression level changes in a colorectal cancer cell line SW480 expressing FOXC2, compared to the pBabe control cells. Genes associated with metastasis regulated by FOXC2 in colorectal cancer were analysed. The role of FOXC2 in breast cancer metastasis are further described in Mani SA, Yang J et al. Mesenchyme Forkhead 1 (FOXC2) plays a key role in metastasis and is associated with aggressive basal-like breast cancers. PNAS 2007; 104: 10069-10074 . A six chip study using total RNA recovered from three separate cultures of SW480/pBabe and three separate cultures of SW480/FOXC2. Each chip measures the expression level of 45033 genes from SW480/pBabe or SW480/FOXC2.
Project description:AP2 transcription factors play important roles in development and cancer, we tried to clarify the role of the so far uncharacterised TFAP2E in colorectal cancer. We used GENE ST 1.0 Arrays to detail up and downregulated target genes of this AP-2 transcription factor. We used the ptarget mammalian expression vector (Promega) to overexpress the TFAP2E gene in the SW480 CRC line.
Project description:In order to comprehensively identify miRNA-expression changes after p53-activation a miRNA-Seq analysis was conducted after activation of a conditional p53 allele in SW480 cells. SW480/pRTR-p53-VSV cells were subjected to miRNA-Seq analysis after 16 hours doxycycline-treatment. Kompetenzzentrum für fluoreszente Bioanalytik, Regensburg, Germany
Project description:To validate the suitability of two commonly used colorectal cancer cell lines, DLD1 and SW480, as model systems to study colorectal carcinogenesis, we treated these cell lines with beta-catenin siRNA and identified beta-catenin target genes using DNA microarrays. The list of identified target genes was compared to previously published beta-catenin target genes found in the PubMed and the GEO databases. Based on the large number of beta-catenin target genes found to be similarly regulated in DLD1, SW480 and LS174T as well as the large overlap with confirmed β-catenin target genes, we conclude that DLD1 and SW480 colon carcinoma cell lines are suitable model systems to study beta-catenin regulated genes and signaling pathways 12 arrays (2 cell lines, 2 treatments, 3 biological replicates)