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Transcription profiling of human colorectal cancer cell lines derived from a primary tumor and a corresponding lymph node metastasis from the same individual

ABSTRACT: SW480 and SW620 are colon cancer cells lines derived from a primary tumor and a corresponding metastasis from the same individual. The numbers indicate the three independent replicate RNA samples processed. Three different software packages were used in parallel for signal calculation: Affymetrix microarray suite 5.0, DNA-Chip analyzer, and Robust multi-array analyses.

ORGANISM(S): Homo sapiens

SUBMITTER: Alessandro Provenzani

PROVIDER: E-GEOD-1323 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Global alterations in mRNA polysomal recruitment in a cell model of colorectal cancer progression to metastasis.

Provenzani Alessandro A Fronza Raffaele R Loreni Fabrizio F Pascale Alessia A Amadio Marialaura M Quattrone Alessandro A

Carcinogenesis 20060310 7

Tumour onset and progression are due to the accumulation of genomic lesions, which alter gene expression and ultimately proteome activities. These lesions are thought to affect primarily the transcriptional control of gene expression. In the present study, we aimed at evaluating the genome-wide occurrence of alterations in the translational control exploiting an isogenic, phenotypically validated cellular model of colorectal cancer (CRC) transition from invasive carcinoma to metastasis. In this ...[more]

PMID: 16531451

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Isogenic primary tumor/metastasis comparison

Project description:SW480 and SW620 are colon cancer cells lines derived from a primary tumor and a corresponding metastasis from the same individual. The numbers indicate the three indipendent replicate RNA samples processed. Three different software packages were used in parallel for signal calculation: Affymetrix microarray suite 5.0, DNA-Chip analyzer, and Robust multi-array analyses. Keywords = metastasis Keywords = colorectal cancer Keywords = tumor progression Keywords: repeat sample

2004-09-01 | GSE1323 | GEO

MicroRNA profiling of human colon cancer cell lines from the primary lesion and lymph node metastatis of the same patient

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.

2009-02-20 | E-MEXP-2060 | biostudies-arrayexpress

miRNAs in colorectal cancer metastasis

Project description:Metastasis is a complex process involving multiple steps. We were interested in the role of microRNAs (miRNAs) in the process of liver colonization by colorectal cancer cells. We hypothesized that the comparison between non-metastatic versus metastatic isogenic cell line should thus offer valuable insight to the molecular mechanisms involved in developing metastatic behavior. KM12C/KM12SM and SW480/SW620 are probably the best available models of isogenic cell lines differing in metastatic properties for colorectal cancer. Our first goal was to identify miRNAs that contribute to the metastatic traits of the isogenic colorectal cancer cell lines, KM12C/KM12SM and SW480/SW620. Total RNA was extracted from cells using the mirVana kit (Ambion). Total RNA (1 µg) from KM12C and SW480 (poorly metastatic) and KM12SM and SW620 (highly metastatic) cells was used to analyze the global miRNA expression profiling with TaqMan Megaplex human array A (v2.0) and B (v3.0) (Applied Biosystems).

2017-03-01 | GSE86302 | GEO

WGBS analysis of various colon cancer cell lines

Project description:We profiled genome-wide DNA methylation in four cancer cell line, ie SW480-lenti SW480-TET2CD, SW620--lenti and SW620-TET2CD.

2020-07-21 | GSE154734 | GEO

Spatial Proteomic Analysis of Isogenic Metastatic Colorectal Cancer Cells Reveals Key Dysregulated Proteins Associated with Lymph Node, Liver and Lung Metastasis

Project description:Liver, lung and lymph nodes are the most common metatastic sites of colorectal cancer (CRC) cells. Here, we aimed to analyze by quantitative spatial proteomics the isogenic KM12 cell system (non-metastatic KM12C cells, liver metastatic KM12SM cells and liver and lung metastatic KM12L4a cells), and the isogenic non-metastatic SW480 and lymph nodes metastatic SW620 cells to study CRC metastasis. Cells were fractionated to study by proteomics five subcellular fractions corresponding to cytoplasm (CEB), membrane (MEB), nucleus (NEB), chromatin-bound proteins (NEB-CBP), and cytoskeletal proteins (PEB), and the secretome. Protein extracts were trypsin digested, labeled with TMT 11-plex and fractionated prior to proteomics analysis on a Q Exactive. We provide data on protein abundance and localization of 4031 proteins in their different subcellular fractions, depicting dysregulation of proteins in abundance and/or localization in the most common sites of CRC metastasis. Alterations in abundance and localization for selected proteins were validated via WB, IF, IHC and ELISA using CRC cells and patients’ tissue and plasma samples. These results supported the relevance of the proteomics results in a real-life scenario of CRC metastasis.

2022-02-22 | PXD030671 | Pride

RNA-seq analysis of various colon cancer cell lines treated with TGFb1 and repsox

Project description:Four cancer cell line, ie SW480-Vector, SW480-TET2, SW620-Vector and SW620-TET2 were treated with tgfb1, repsox and control. Then the total RNA of these samples were extracted and sequenced with Illumina Nextseq 500.

2020-07-18 | GSE154646 | GEO

Targeting Lymph Node Sinus Macrophages to Inhibit Lymph Node Metastasis.

Project description:Lymph nodes are important peripheral immune organs in which numerous important immune responses occur. During the process of lymphatic metastasis, lymph nodes are also sites through which tumor cells must pass. Therefore, it is essential to develop a drug delivery system that can specifically transfer immunostimulatory medicine into lymph nodes to block lymphatic metastasis. Here, we developed a nucleic acid drug delivery system containing cationic agarose (C-agarose) and CpG oligodeoxynucleotides. C-agarose has a high affinity for Siglec-1 on the surface of lymph node sinus macrophages, which have a high specificity for targeting lymph nodes. Subcutaneous implantation of C-agarose+CpG gel caused the accumulation of CpG in the lymph node sinus macrophages and generated antitumor immune responses in the lymph node. C-agarose+CpG gel treatment decreased the metastasis size in the tumor-draining lymph node (TDLN) and lung metastatic nodules and suppressed tumor growth in both a mouse 4T1 breast cancer model and a B16F10 melanoma model. On this basis, this study proposes a nonsurgical invasive lymph node targeting immunotherapy concept that may provide a new approach for antitumor metastasis.

| S-EPMC6529739 | biostudies-literature

Transcription profiling of two human colon cancer cell lines derived from a primry tumor and a lypmh node metastatsis from a single patient reveals global alterations in mRNA polysomal recruitment in a cell model of colorectal cancer progression to metastasis.

Project description:Two colon cancer cell lines are under study. SW480 and SW620. The first one is derived from primary cancer, SW620 are from lymphnode metastatic sites. they both come from the sample patient. Polysomal RNA fractions from the two isogenic colon cancer cells lines was purified by sucrose gradient and hybridized on affymetrix hgu133a chips. this study is complementary to the series GSE1323 where total RNA was used instead. Comparison between the polysomal fraction chips and the total RNA chips is performed and the analysis proposed in a paper from the authors (at the moment in preparation).

2007-10-27 | E-GEOD-2509 | biostudies-arrayexpress

MicroRNA expression profile between human colorectal cancer SW480 and SW620 cell line

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.

2016-08-01 | GSE72412 | GEO

Genes that mediate colorectal cancer liver metastasis

Project description:The study identifies a set of genes through functional selection in an orthotopic colorectal cancer mouse model that play an important role in mediating colorectal cancer liver metastasis. We look at the gene profiling of metastatic colorectal cancer cells (L1 and L2) and non-mestastatic colorectal cancer cells (sw620 and sw480) using Affymetrix U133A oligonucleotide arrays.

2011-12-31 | GSE30687 | GEO

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