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Proteomic characterization of transcription and splicing factors associated with a more invasive phenotype in colorectal cancer

ABSTRACT: To find new transcription and splicing factors associated with the metastatic phenotype we used a concatenated tandem array of consensus transcription factors response elements (catTFRE) on nuclear extracts of colon cancer cell lines. We used two different isogenic pairs of colorectal metastatic cells, KM12SM/KM12C and SW620/480. Proteins were pulled-down using biotinylated DNA sequences and streptavidin beads and analyzed by LC-MSMS.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell, Cell Culture

DISEASE(S): Colon Cancer

SUBMITTER: Consuelo Marín-Vicente

LAB HEAD: J. Ignacio Casal Alvarez

PROVIDER: PXD006662 | Pride | 2017-11-15

REPOSITORIES: Pride

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Proteomic Characterization of Transcription and Splicing Factors Associated with a Metastatic Phenotype in Colorectal Cancer.

Torres Sofía S García-Palmero Irene I Marín-Vicente Consuelo C Bartolomé Rubén A RA Calviño Eva E Fernández-Aceñero María Jesús MJ Casal J Ignacio JI

Journal of proteome research 20171121 1

We investigated new transcription and splicing factors associated with the metastatic phenotype in colorectal cancer. A concatenated tandem array of consensus transcription factor (TF)-response elements was used to pull down nuclear extracts in two different pairs of colorectal cancer cells, KM12SM/KM12C and SW620/480, genetically related but differing in metastatic ability. Proteins were analyzed by label-free LC-MS and quantified with MaxLFQ. We found 240 proteins showing a significant dysregu ...[more]

PMID: 29131639

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Proteomic analysis of serum EVs derived from PSC, CCA and PSC-CCA patients

Project description:Cholangiocarcinomas (CCAs) are heterogeneous biliary cancers with dismal prognosis. Their etiologies remain mostly unclear, although primary sclerosing cholangitis (PSC) is a well-known risk factor. There is an urgent need of accurate non-invasive biomarkers for early CCA diagnosis and to predict patient´s prognosis, which may improve their clinical management and outcome. Here, by high-throughput proteomic analysis of serum extracellular vesicles (EVs), we identified diagnostic and/or prognostic biomarkers specific for CCAs in patients with PSC, and others common to all CCA subtypes. Bulk RNA tissue transcriptomic data revealed that these biomarkers are predominantly expressed in hepatobiliary tissues, being expressed in different liver cell types. Furthermore, single-cell RNAseq (scRNA-seq) analysis revealed that the expression of these biomarkers was preferentially found in malignant cholangiocytes within CCA tumors. In summary, these results highlight the potential of serum EVs to reflect cancer presence, especially for difficult-to-diagnose malignancies, including CCA."

2023-07-20 | PXD026197 | Pride

Aryl hydrocarbon receptor-interacting protein regulates tumorigenic and metastatic properties of colorectal cancer cells driving liver metastasis

Project description:Aryl hydrocarbon receptor-interacting protein (AIP), a putative positive intermediary in aryl hydrocarbon receptor-mediated signaling, is overexpressed in highly metastatic human KM12SM CRC cells, with high metastatic capacity to liver, and other highly metastatic CRC cells. Meta-analysis and immunohistochemistry were used to assess the relevance of this protein in CRC. Cellular functions and signaling mechanisms mediated by AIP were assessed by gain-of-function experiments and in vitro and in vivo experiments. A significant association of high AIP expression with poor CRC patients’ survival was observed. Gain-of-function and quantitative proteomics experiments demonstrated that AIP increased tumorigenic and metastatic properties of isogenic KM12C (poorly-metastatic) and KM12SM CRC cells. AIP overexpression dysregulated epithelial-to-mesenchymal (EMT) markers and induced several transcription factors and Cadherin-17 activation. The former induced the signaling activation of AKT, SRC, and JNK kinases to increase adhesion, migration and invasion of CRC cells. In vivo, AIP expressing KM12 cells induced tumor growth and liver metastasis. Furthermore, KM12C (poorly-metastatic) cells ectopically expressing AIP became metastatic to liver. Our data reveal new roles for AIP in regulating proteins associated with cancer and metastasis to induce tumorigenic and metastatic properties in colon cancer cells driving liver metastasis.

2023-05-10 | PXD031119 | Pride

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

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2015-12-14 | PXD001451 | Pride

The extracellular proteome of two Bifidobacterium strains reveals different adaptation strategies to low iron conditions

2015-12-14 | PXD001452 | Pride

Comparative proteomics of Mycoplasma pneumoniae clinical isolates

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2016-07-05 | PXD002501 | Pride

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