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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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Dataset's files

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			Action	DRS
	KM12C_a-01.msf	Msf
	KM12C_a.mgf	Mgf
	KM12C_a.raw	Raw
	KM12C_b-01.msf	Msf
	KM12C_b.mgf	Mgf

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Publications

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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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

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

Functional proteomics characterization of the role of SPRYD7 in colorectal cancer progression and metastasis

Project description:SPRY domain-containing protein 7 (SPRYD7) is a barely known protein identified by spatial proteomics as upregulated in highly-metastatic to liver KM12SM colorectal cancer (CRC) cells in comparison to its isogenic poorly-metastatic KM12C CRC cells. Here, we aimed at analyzing SPRYD7 role in CRC by functional proteomics. By immunohistochemistry, the overexpression of SPRYD7 was observed to be associated to poor survival of CRC patients, and to an aggressive and metastatic phenotype. SPRYD7 stably overexpression was performed in KM12C and SW480 poorly-metastatic CRC cells, and in their isogenic highly-metastatic to liver KM12SM and to lymph nodes SW620 CRC cells, respectively. After confirming the upregulation of SPRYD7, in vitro and in vivo functional assays confirmed a key role of SPRYD7 in proliferation and migration of CRC cells. Furthermore, SPRYD7 was observed as an inductor of angiogenesis. In addition, the dysregulated SPRYD7-associated proteome and SPRYD7 interactors were elucidated by 10-plex TMT quantitative proteins, immunoproteomics, and bioinformatics. After WB validation, the biological pathways associated to the stably overexpression of SPRYD7 were visualized. In conclusion, it was demonstrated here that SPRYD7 is a novel protein associated to CRC progression and metastasis. Thus, SPRYD7 and its interactors might be of relevance to identify novel therapeutic targets for advanced CRC.

2024-01-26 | PXD042874 | Pride

Functional proteomics characterization of the role of SPRYD7 in colorectal cancer progression and metastasis

2024-01-26 | PXD042901 | Pride

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

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

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

Project description:B. kashiwanohense PV20-2 and B. pseudolongum PV8-2 are strains isolated from breast fed iron deficient Kenyan infants, selected for their high iron sequestration mechanisms and their genome was completely sequenced. Based on their high iron sequestration features we hypothesized that B. kashiwanohense PV20-2 and B. pseudolongum PV8-2, possess iron related genes and excrete iron binding proteins in the culture media under iron limited conditions. Thus, the complete genomes of B. kashiwanohense PV20-2 and B. pseudolongum PV8-2 were compared to other bifidobacterial genomes to identify genes potentially involved in iron metabolism and the coding sequences from the genome were used as a scaffold to identify the extracellular proteome of both strains grown under low iron conditions using a gel-based shotgun proteomic approach.

2015-12-14 | PXD001452 | Pride

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

2015-12-14 | PXD001451 | Pride

Cilia and the exocyst are involved in urinary extracellular vesicle production and content

Project description:A recently proposed model of cell-cell communication, called “urocrine signaling”, hypothesizes that small (50-150 mm) extracellular vesicles (EVs) carry signals to “downstream” kidney tubule cells. We previously showed that the exocyst, a highly-conserved eight-protein (Exoc1-8) trafficking complex, is necessary for ciliogenesis, we show that the EV number released from MDCK cells was increased in EXOC5 OE, while it was decreased in Exoc5 KD, compared to control. To determine how Exoc5 changes the composition of EVs, we isolated EVs from Exoc5 control, KD, and OE MDCK cells, and subjected them mass spectrometry-based proteomic analysis to determine the protein composition of the EVs. By dendrogram, heat map, and principle component analysis, the protein content of the EVs was significantly different in Exoc5 KD, EXOC5 OE, and control MDCK cells. To confirm the proteomic results, we examined, by Western blot analysis, expression of the small guanosine triphosphate (GTP)-binding protein ADP-ribosylation factor (Arf6) and the epidermal growth factor receptor kinase substrate 8-like protein 2 (Eps8L2).

2019-11-06 | PXD013549 | Pride

Mouse bone marrow derived neutrophils, LC-MSMS

Project description:Analysis of cell membrane-enriched proteins of mouse polymorphonuclear neutrophils. Further related data are present in project <a href="http://www.ebi.ac.uk/pride/archive/projects/PXD003015">PXD003015</a>.

2015-07-20 | PXD002244 | Pride

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