Colorectal cancer cell-derived microvesicles are enriched in cell cycle-related mRNAs that promote proliferation of endothelial cells
- Bok Sil Hong†1,
- Ji-Hoon Cho†2,
- Hyunjung Kim1,
- Eun-Jeong Choi1,
- Sangchul Rho2,
- Jongmin Kim2,
- Ji Hyun Kim1,
- Dong-Sic Choi1,
- Yoon-Keun Kim1,
- Daehee Hwang2, 3Email author and
- Yong Song Gho1, 2Email author
© Hong et al; licensee BioMed Central Ltd. 2009
Received: 30 June 2009
Accepted: 25 November 2009
Published: 25 November 2009
Various cancer cells, including those of colorectal cancer (CRC), release microvesicles (exosomes) into surrounding tissues and peripheral circulation. These microvesicles can mediate communication between cells and affect various tumor-related processes in their target cells.
We present potential roles of CRC cell-derived microvesicles in tumor progression via a global comparative microvesicular and cellular transcriptomic analysis of human SW480 CRC cells. We first identified 11,327 microvesicular mRNAs involved in tumorigenesis-related processes that reflect the physiology of donor CRC cells. We then found 241 mRNAs enriched in the microvesicles above donor cell levels, of which 27 were involved in cell cycle-related processes. Network analysis revealed that most of the cell cycle-related microvesicle-enriched mRNAs were associated with M-phase activities. The integration of two mRNA datasets showed that these M-phase-related mRNAs were differentially regulated across CRC patients, suggesting their potential roles in tumor progression. Finally, we experimentally verified the network-driven hypothesis by showing a significant increase in proliferation of endothelial cells treated with the microvesicles.
Our study demonstrates that CRC cell-derived microvesicles are enriched in cell cycle-related mRNAs that promote proliferation of endothelial cells, suggesting that microvesicles of cancer cells can be involved in tumor growth and metastasis by facilitating angiogenesis-related processes. This information will help elucidate the pathophysiological functions of tumor-derived microvesicles, and aid in the development of cancer diagnostics, including colorectal cancer.
During growth or activation, a variety of cell types, including hematopoietic, epithelial, and tumor cells, shed small membrane vesicles called microvesicles (exosomes) [1–6]. These microvesicles, which are 30-200 nm in diameter, are derived from the endosomal membrane compartment following the fusion of multivesicular bodies with the plasma membrane. Cells also release microvesicles directly by the outward budding of the plasma membrane in a calcium-dependent manner . Microvesicles have been also found in various body fluids, such as plasma, malignant pleural effusion, and urine [7–10]. The numerous proteins and bioactive lipids contained in microvesicles differ in composition depending on the types and states of donor cells. Recent studies have reported that microvesicles also contain mRNA [11–15]. Although their biological roles are not completely understood, microvesicles have been shown to stimulate target cells by transferring microvesicular components (e.g., plasma membrane receptors and bioactive lipids) into target cells, transferring infectious particles, such as human immunodeficiency virus and prions, and delivering microvesicular mRNAs to target cells (called horizontal transfer of genetic materials), where they are translated into functionally active proteins [12–15]. These findings suggest that microvesicles are not cellular debris but are communicasomes, which are extracellular organelles with distinct roles in intercellular communication [5, 16].
Colorectal cancer (CRC) is one of the most frequent malignant tumors in Western countries . CRC cells also release microvesicles [5, 18], and the revelation from proteomic studies that CRC cell-derived microvesicles contain several hundred proteins has helped elucidate the functions of microvesicles at the protein level [5, 18]. It has also been reported that RNA-lipid complexes are released from the plasma membrane of CRC cells, and CRC patients show significantly elevated serum mRNA levels over those of healthy subjects [19, 20]. In view of the higher concentration of RNase in the serum of patients with cancer, these circulating mRNAs are likely to be present in a particle-associated form [21, 22]. Collectively, these observations suggest that CRC cell-derived microvesicles carry mRNA, together with proteins and lipids, which may exert a functional influence on CRC-related processes.
To improve the understanding of the potential roles of CRC cell-derived microvesicles in CRC-related processes, we conducted a systems approach to the CRC cell-derived microvesicles using transcriptome analysis of the microvesicles derived from SW480 cells, a human CRC cell line, and the donor CRC cells. Our systems approach to CRC cell-derived microvesicles provided 11,327 microvesicular transcripts that are involved in various tumor-related processes, which suggests that the microvesicles reflect the physiology of the donor CRC cells. Furthermore, we found that CRC-derived microvesicles enriched with cell cycle-related mRNAs that showed differential expression patterns in CRC patient data. Moreover, microvesicles stimulated proliferation of endothelial cells, suggesting that CRC-derived microvesicles can be involved in tumor growth and metastasis by facilitating angiogenesis-related processes. Our results provide a number of indicators that will not only increase the understanding of pathophysiological functions of tumor derived microvesicles, but also may stimulate the development of novel methods for cancer diagnostics including CRC.
Purification and characterization of microvesicles derived from human SW480 cells
Transcriptomic analysis of microvesicles
Cellular processes overrepresented by the microvesicular mRNAs
Enrichment of cell cycle-related mRNAs in microvesicles
To predict the potential roles of the 27 cell cycle-related microvesicle-enriched genes at the molecular level, we then reconstructed a biological network (Figure 5C) describing the overrepresented cell cycle-related processes (Figure 5D). The network was reconstructed using the 27 genes belonging to the cell cycle GO term and their first and second interaction neighbors obtained from HPRD, BIND, and BioGRID interaction databases. In the network, yellow nodes represent the 27 microvesicle-enriched genes, 20 of which closely interact with cell cycle-related processes. The network shows that the microvesicle-enriched genes closely interact with key pathways in the cell cycle, including cyclin-dependent kinases 8 and N3 (CDK8 and CDKN3), centrosomal protein 55 kilodaltons (CEP55), kinensin family members (KIF15 and KIF23), centromere proteins (CENPE and CENPF), anillin (ANLN), PDZ-binding kinase (PBK), and NIMA-related kinase 2 (NEK2). Collectively, these observations suggest that the microvesicle-enriched genes may contribute to the increased cell proliferation of target cells during tumor progression by modulating activities of cell cycle-related pathways.
To examine the clinical implications of the 241 microvesicle-enriched genes, we collected from the GEO database  two transcriptomic datasets (GSE2109 and GSE5206), including global mRNA measurements from CRC patients at various stages, and then used cluster analysis to investigate whether these genes are differentially expressed among patients (additional file 6). Interestingly, a cluster comprising 36 of the 241 microvesicle-enriched genes showed consistent differential expression patterns across the patients in the two independent datasets (Figure 5D): the expression levels of the genes in each patient sample were compared to their average expression levels in the individual datasets. Of these, 15 of the 36 genes showing differential expression patterns are involved in M-phase-related processes (red box in Figure 5B; e.g., spindle formation, kinetochore assembly, chromosome segregation, and cytokinesis) that are either involved in or interact with components involved in the M-phase of the mitotic cell cycle (see diamond nodes in Figure 5C and additional file 7). Note that 17 of the 36 genes belong to cell cycle GOBP. These observations suggest that microvesicle-enriched genes reflect their potential roles in tumor progression in patients with CRC.
Stimulation of endothelial cell proliferation by microvesicles
This study presents a transcriptomic analysis of CRC cell-derived microvesicles, among which we identified 11,327 microvesicular transcripts involved in various tumor-related processes that reflect the physiology of the donor CRC cells. Among these transcripts, we found 241 mRNAs enriched in microvesicles beyond their levels in donor cells, of which 27 were involved in the cell cycle. Moreover, 20 of these 27 mRNAs were associated with cell cycle M-phase activities, and 15 of these showed differential expression patterns in CRC patient data. We then demonstrated that these mRNAs may modulate activities of M-phase processes during the cell cycle by reconstructing a cell cycle network, which showed that the corresponding proteins belong to and also interact with those involved in M-phase-related processes. To experimentally verify this network-driven hypothesis, we demonstrated that CRC cell-derived microvesicles are delivered to endothelial cells and stimulate the proliferation of endothelial cells. Since this proliferation is an essential step in neovascularization, our finding suggests that microvesicles have angiogenic activities.
The preparation of microvesicles that are not contaminated with cellular debris, bovine serum-derived microvesicles, or any non-microvesicular mRNA is critical for transcriptional profiling of microvesicles. As the half-life of individual microvesicular mRNA transcripts is unknown, the rapid analysis of microvesicular mRNA is also very important. We therefore followed our previously described purification methods with the following two major modifications . In particular, RNase A treatment was applied in order to degrade non-microvesicular RNA derived from damaged cells or leaky microvesicles (Figure 1A). The microvesicles were finally purified using iodixanol density gradient centrifugation, which is much faster than the conventional sucrose density gradient centrifugation [14, 25]. As a result, the high quality of the microvesicular RNA was obtained as indicated by the Bioanalyzer results (RIN: 8.7).
Growing evidence indicates that tumor-derived microvesicles are involved in tumor progression via the modulation of tumorigenesis, angiogenesis, immune response, invasion, and metastasis [1–5]. Moreover, recent studies have reported that microvesicular mRNA can induce potent epigenetic changes in target cells, as microvesicular mRNA is delivered to target cells, where it is translated into functionally active proteins [11–14]. Our findings that SW480-derived microvesicular mRNAs are involved in various tumor-related processes (Figure 4 and Figure 5) and SW480-derived microvesicles can initiate angiogenesis via the stimulation of endothelial cell proliferation (Figure 6) also suggest that the microvesicular mRNAs play potential roles in progression of CRC. Furthermore, SW480-derived microvesicles are enriched with CENPE, KIF15, CEP55, CCNA2, NEK2, PBK, and CDK8 (Figure 6a) that are M-phase-related transcripts involved in tumorigenesis and tumor progression [26–28]. Although we could not exclude the other possibility, our observations suggest that SW480-derived microvesicles promote the proliferation of endothelial cells by increasing their cell cycle activities via the horizontal transfer of these M-phase-related microvesicular mRNAs. Further studies on microvesicles derived from other colon cancer cells would provide valuable data. Thus, the inhibition of either microvesicle shedding or modulation of microvesicular function has been proposed as worthwhile approaches to cancer therapy. Recently, Al-Nedawi et al. (2009) showed that the treatment of Diannexin, which inhibits the uptake of the A431 (human squamous cell carcinoma cell line)-derived microvesicles into endothelial cells, to A431 tumor xenografts in mice led to a reduction of tumor growth rate and microvascular density . Thus, our findings above suggest that the inhibition of biogenesis, trafficking or function of the CRC-derived microvesicles also can offer a novel therapeutic approach for CRC.
Despite the progress in understanding and treating CRC, it remains a leading cause of mortality worldwide . A significant improvement in survival would be expected with early diagnosis of CRC. Several studies have reported that the level of tumor-derived microvesicles is elevated significantly in the serum or the ascites fluid of cancer patients [8, 31, 32]. Recently, Taylor et al. proposed that microRNA profiling of circulating tumor microvesicles could potentially be used to identify diagnostic markers for human ovarian cancer . Thus, our finding that the microvesicular mRNA reflects the mRNA signature of the parental CRC suggests that the microvesicular mRNA may be a useful diagnostic and/or prognostic marker of early stage cancer and could be evaluated in a non-invasive manner. Possible CRC marker candidates can be predicted as the microvesicle-enriched mRNAs that show colon-specific expression patterns (additional file 9).
These study present potential roles of CRC cell-derived microvesicles in tumor progression via a global comparative microvesicular and cellular transcriptomic analysis of human SW480 CRC cells. However, it is not clear how these microvesicular mRNAs cooperatively act with other microvesicular components such as lipids and proteins in the target cells. Future studies on collective pathophysiological roles of such microvesicular components in modulating dynamically tumor-related networks in the target cells will be valuable in clarifying the microvesicle-involved communication, including that in human CRC, and further unraveling the complexity of the intercellular communication involved in tumorigenesis, angiogenesis, and metastasis.
SW480 (human colorectal adenocarcinoma cells) and THP-1 (human acute monocytic leukemia cells) were cultured in RPMI-1640 medium (Invitrogen Corporation, Carlsbad, CA) supplemented with 10% heat-inactivated fetal bovine serum (Invitrogen Corporation), 100 U/mL penicillin, and 0.1 mg/ml streptomycin. human umbilical vein endothelial cells (HUVECs) were isolated from freshly delivered umbilical cords and maintained as described previously .
Purification of microvesicles
The SW480 cells were washed twice with PBS and then incubated in serum-free RPMI-1640. After 24 h incubation, the conditioned medium was collected, centrifuged at 500 × g for 10 minutes, and then centrifuged twice at 2,000 × g for 15 minutes. The supernatant was concentrated using a QuixStand Benchtop System (GE Healthcare, Bucks, UK) with a 100-kilodaltons hollow fiber membrane (GE Healthcare), placed upon 0.5 mL of 0.8 and 2.0 M sucrose cushions in buffer (20 mM HEPES, 150 mM NaCl, pH 7.4), and then centrifuged at 100,000 × g for 2 hours. The microvesicles were harvested from the interface between the 0.8 and 2.0 M sucrose cushions. After treatment with 20 μg/ml RNase A (Roche Diagnostics, Mannheim, Germany) for 30 minutes at room temperature, the sample was diluted 10-fold in PBS, placed upon 0.35 ml of 0.8 M and 0.15 ml of 2.0 M sucrose cushions, and centrifuged at 100,000 × g for 2 hours. The microvesicles were harvested and mixed with an equal volume of 60% iodixanol solution (Axis-Shield PoC AS, Oslo, Norway), to give 30% iodixanol. This sample was placed at the bottom of a tube and overlaid with 20% and 5% iodixanol. After centrifugation at 200,000 × g for 2 hours, 10 fractions of equal volume were removed from the top of the gradient. The microvesicle-enriched fraction was diluted with 9 ml of PBS and then centrifuged at 100,000 × g for 2 hours. Finally, the purified microvesicles were resuspended in PBS and used immediately for the preparation of microvesicular RNA.
Transmission electron microscopy
The purified microvesicles were applied to glow-discharged carbon-coated copper grids (EMS, Matfield, PA). After allowing the microvesicles to absorb for 3 minutes, the grids were rinsed with droplets of de-ionized water and positive-stained with a mixture of 2% methylcellulose and 4% uranylacetate (Ted Pella, Redding, CA). Electron micrographs were recorded using a JEM 1011 microscope (Jeol, Japan) at an acceleration voltage of 100 kilovolt.
Whole cell lysate and microvesicles were separated by SDS-PAGE and then transferred to a polyvinylidene defluoride membrane. The membrane was blocked, incubated with antibodies followed by secondary antibodies conjugated to horseradish peroxidase and subjected to enhanced chemiluminescence.
Preparation of total RNA and reverse-transcription polymerase chain reaction
Total RNA was extracted from SW480 cells and purified microvesicles by a single-step isolation method using TRIzol reagent (Invitrogen Corporation). The RNA was re-suspended in diethyl pyrocarbonate-treated water and quantified by UV absorbance at 260/280 nm. Reverse-transcription polymerase chain reaction (RT-PCR) was performed with 100 ng of total RNA and 100 nM forward and reverse primers, using a One Step SYBR RT-PCR kit (Takara, Otsu, Japan). The primer sequences are provided in additional file 10. A LightCycler system (Roche Diagnostics, Mannheim, Germany) was used with the following thermal profile: initial denaturation at 95°C for 10 minutes, followed by 45 cycles of 95°C for 15 seconds, 60°C for 15 seconds, and 72°C for 10 seconds.
For transcriptional profiling, we used Illumina Human-6 v2 Expression BeadChips (Illumina, San Diego, CA), which include a bead pool of ~48,000 unique bead types corresponding to 47,294 transcripts . The quality of the cellular and microvesicular total RNA was analyzed using an Agilent 2100 Bioanalyzer. 640 ng of total RNA from the microvesicles and SW480 cells were reverse-transcribed and amplified, according to the protocols in the Illumina TotalPrep RNA amplification kit manual (Ambion, Austin, TX). Then, in vitro transcription was carried out to generate complementary RNAs. 1.5 μg of complementary RNAs was hybridized onto each array (four replicates for the microvesicles and SW480 cells) and then labeled with Cy3-streptavidin (Amersham Biosciences, Little Chalfont, UK). The array was then scanned using a Bead Station (Illumina). The full dataset was submitted to Gene Expression Omnibus (GEO) under submission number GSE9589. The probe intensities for the microvesicles and SW480 cells were separately normalized using quantile normalization in beadarray 1.6, an R/Bioconductor package . The probes were annotated using lumi 1.4, an R/Bioconductor package. To determine present probes, we applied the following Gaussian mixture modeling method ; 1) two Gaussian probability density functions, one for the absent probes and the other for the present ones, were fitted to the distribution of the observed probe intensity; and 2) the probes whose maximum intensities in all four replicates were higher than the threshold intensity (α: the intensity where two fitted Gaussian probability density functions meet) were determined to be present. Also, the microvesicles-enriched mRNAs were identified as the ones showing more than 2-fold changes between the median intensities of four replicates in microvesicles than those in SW480 cells. For a comparison of the microvesicular mRNAs in this study with those from the previous two studies of glioblastoma- and mouse mast cell (MC/9)-derived microvesicles [13, 14], we used Affymetrix/Illumina annotation information (GPL1261, GEO accession), human-WG6 annotation, and human and mouse orthology from Mouse Genome Informatics (MGI 4.0, http://www.informatics.jax.org).
Functional enrichment analysis and network analysis
We used BiNGO version 2.0, a Cytoscape plug-in , to identify biological processes overrepresented by the mRNAs detected in the microvesicles (also by the the microvesicle-enriched mRNAs). In a Gene Ontology (GO) tree, each node and node color represent the corresponding enriched Gene Ontology Biological Processes (GOBP) and the associated statistical significance (P values computed from a hypergeometric hypothesis test in BiNGO), respectively. To describe the cell cycle related processes in which the microvesicle-enriched mRNAs are involved and the interactions among the proteins corresponding to such mRNAs, we reconstructed an initial biological network using the proteins and their first and second neighbors , obtained from BIND http://www.bind.ca, HPRD http://hprd.org, and BioGrid http://www.thebiogrid.org databases, to include as many as the 27 cell cycle related microvesicle-enriched genes. To generate a compact network (Figure 4B) from the complex initial network, we then removed the nodes that were not connected with the 27 microvesicle-enriched genes, but kept the nodes whose removal would disconnect the 27 microvesicle-enriched genes from the main network.
Purified microvesicles were labeled with PKH26 red fluorescent labeling kit (Sigma-Aldrich, St. Louis, MO) according to the manufacturer's instructions. The labeled microvesicles (1 μg/ml) were allowed to bind for 1 hour at 4°C, washed with PBS, and then incubated at 37°C for 24 hours. Cells were fixed with 4% paraformaldehyde, washed, and stained with calnexin (endoplasmic reticulum marker protein). The uptake of labeled microvesicles by HUVECs was determined using an FV1000 confocal microscope (Olympus, Tokyo, Japan) equipped with a UPlanSApo 40×/0.75 objective lens of red fluorescence intensity.
HUVECs grown on 0.1% gelatin-coated glass coverslips were incubated with microvesicles (1 μg/ml) for the indicated times. The cells were fixed with 4% paraformaldehyde, permeablilized with 0.2% Triton X-100, and then incubated with anti-phospho-histone H3 (Ser 10) (Upstate Biotechnology, Lake Placid, NY) and anti-α-tubulin antibodies (Sigma-Aldrich). After treatment with AlexaFluor-conjugated secondary antibodies (Invitrogen Corporation), the cells were counterstained with Hoechst (Sigma-Aldrich). The FV1000 Olympus confocal microscope was used for the analysis.
The full dataset is submitted to Gene Expression Omnibus under submission number series, GSE9589.
human umbilical vein endothelial cells
reverse-transcription polymerase chain reaction
Gene Expression Omnibus
gene ontology biological processes
The Korea Science and Engineering Foundation (KOSEF) funded by the Korea government (MEST) R15-2004-033-07002-0 and R15-2004-033-05001-0; and the 21C Frontier Functional Proteomics Project from MEST FPR08B1-240 and FPR08A1-050.
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