scholarly journals Qualitative and quantitative top-down proteomics of human colorectal cancer cell lines identified 23000 proteoforms and revealed drastic proteoform-level differences between metastatic and non-metastatic cancer cells

2021 ◽  
Author(s):  
Elijah N. McCool ◽  
Tian Xu ◽  
Wenrong Chen ◽  
Nicole C. Beller ◽  
Scott M. Nolan ◽  
...  

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.

2011 ◽  
Vol 10 (10) ◽  
pp. 4373-4387 ◽  
Author(s):  
Dipanjana Ghosh ◽  
Han Yu ◽  
Xing Fei Tan ◽  
Teck Kwang Lim ◽  
Ramdzan M. Zubaidah ◽  
...  

Molecules ◽  
2021 ◽  
Vol 26 (5) ◽  
pp. 1261
Author(s):  
Nurul Fattin Che Rahim ◽  
Yazmin Hussin ◽  
Muhammad Nazirul Mubin Aziz ◽  
Nurul Elyani Mohamad ◽  
Swee Keong Yeap ◽  
...  

Colorectal cancer (CRC) is the third most common type of cancer worldwide and a leading cause of cancer death. According to the Malaysian National Cancer Registry Report 2012–2016, colorectal cancer was the second most common cancer in Malaysia after breast cancer. Recent treatments for colon cancer cases have caused side effects and recurrence in patients. One of the alternative ways to fight cancer is by using natural products. Curcumin is a compound of the rhizomes of Curcuma longa that possesses a broad range of pharmacological activities. Curcumin has been studied for decades but due to its low bioavailability, its usage as a therapeutic agent has been compromised. This has led to the development of a chemically synthesized curcuminoid analogue, (2E,6E)-2,6-bis(2,3-dimethoxybenzylidine) cyclohexanone (DMCH), to overcome the drawbacks. This study aims to examine the potential of DMCH for cytotoxicity, apoptosis induction, and activation of apoptosis-related proteins on the colon cancer cell lines HT29 and SW620. The cytotoxic activity of DMCH was evaluated using the [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide] (MTT) cell viability assay on both of the cell lines, HT29 and SW620. To determine the mode of cell death, an acridine orange/propidium iodide (AO/PI) assay was conducted, followed by Annexin V/FITC, cell cycle analysis, and JC-1 assay using a flow cytometer. A proteome profiler angiogenesis assay was conducted to determine the protein expression. The inhibitory concentration (IC50) of DMCH in SW620 and HT29 was 7.50 ± 1.19 and 9.80 ± 0.55 µg/mL, respectively. The treated cells displayed morphological features characteristic of apoptosis. The flow cytometry analysis confirmed that DMCH induced apoptosis as shown by an increase in the sub-G0/G1 population and an increase in the early apoptosis and late apoptosis populations compared with untreated cells. A higher number of apoptotic cells were observed on treated SW620 cells as compared to HT29 cells. Human apoptosis proteome profiler analysis revealed upregulation of Bax and Bad proteins and downregulation of Livin proteins in both the HT29 and SW620 cell lines. Collectively, DMCH induced cell death via apoptosis, and the effect was more pronounced on SW620 metastatic colon cancer cells, suggesting its potential effects as an antimetastatic agent targeting colon cancer cells.


2021 ◽  
Vol 22 (4) ◽  
pp. 1886
Author(s):  
Jun Nakayama ◽  
Yuxuan Han ◽  
Yuka Kuroiwa ◽  
Kazushi Azuma ◽  
Yusuke Yamamoto ◽  
...  

Metastasis is a complex event in cancer progression and causes most deaths from cancer. Repeated transplantation of metastatic cancer cells derived from transplanted murine organs can be used to select the population of highly metastatic cancer cells; this method is called as in vivo selection. The in vivo selection method and highly metastatic cancer cell lines have contributed to reveal the molecular mechanisms of cancer metastasis. Here, we present an overview of the methodology for the in vivo selection method. Recent comparative analysis of the transplantation methods for metastasis have revealed the divergence of metastasis gene signatures. Even cancer cells that metastasize to the same organ show various metastatic cascades and gene expression patterns by changing the transplantation method for the in vivo selection. These findings suggest that the selection of metastasis models for the study of metastasis gene signatures has the potential to influence research results. The study of novel gene signatures that are identified from novel highly metastatic cell lines and patient-derived xenografts (PDXs) will be helpful for understanding the novel mechanisms of metastasis.


Cancers ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1641
Author(s):  
Josep Tarragó-Celada ◽  
Marta Cascante

Metabolic adaptation is emerging as an important hallmark of cancer and metastasis. In the last decade, increasing evidence has shown the importance of metabolic alterations underlying the metastatic process, especially in breast cancer metastasis but also in colorectal cancer metastasis. Being the main cause of cancer-related deaths, it is of great importance to developing new therapeutic strategies that specifically target metastatic cells. In this regard, targeting metabolic pathways of metastatic cells is one of the more promising windows for new therapies of metastatic colorectal cancer, where still there are no approved inhibitors against metabolic targets. In this study, we review the recent advances in the field of metabolic adaptation of cancer metastasis, focusing our attention on colorectal cancer. In addition, we also review the current status of metabolic inhibitors for cancer treatment.


2011 ◽  
Vol 29 (4_suppl) ◽  
pp. 444-444 ◽  
Author(s):  
W. He ◽  
S. C. Wong ◽  
B. Ma ◽  
S. S. NG ◽  
M. Y. Lam ◽  
...  

444 Background: Wnt signaling is well known for its role in colorectal cancer (CRC) formation through transcriptional activities of nuclear β-catenin. Although activation of Wnt signaling depends on specific Wnt/Frizzled receptors (FZD) combinations, the specificity of the interaction and the role of FZD in that particular interaction are still unknown. Among the 10 Wnt receptors of the FZD protein family, FZD-3 is involved in neurodevelopmental abnormalities and gastric cancer carcinogenesis. However, the expression of FZD-3 in CRC is not clear. Therefore in this study, we examined the expression of FZD-3 in CRC cell lines and CRC patient tissues with various pathological stages. The information obtained will be important for us to understand the role of FZD-3 in the development of CRC. Methods: FZD-3 mRNA expression was studied in CRC metastatic SW620, primary SW480 and normal CCD18co cell lines using quantitative real-time polymerase chain reaction with primers and a Taqman minor grove binder probe (Applied Biosystems, Foster City, USA). Moreover, paraffin-embedded specimens of 40 CRC patient tissues, 25 colorectal adenoma (CA) tissues were retrieved from the Department of Pathology, Queen Elizabeth Hospital, Hong Kong Special Administrative Region for FZD-3 immunostaining using an anti-FZD-3 antibody (Catalog no: MAB1001, R&D systems Inc., Minneapolis, USA) in an automatic Ventana Benchmark XT immunostainer (Ventana Medical Systems Inc., Tucson, USA). Results: FZD-3 mRNA was up-regulated in metastatic SW620 cell line (fold-change: 622) and in primary SW480 cell line (fold-change: 820) when compared to that in normal CCD18co cell line. Furthermore, immunostaining showed that FZD-3 protein was expressed in 100% (40/40) of CRC specimens and 84% (21/25) of CA specimens. Detailed analysis showed that FZD-3 protein was significantly up-regulated in CRC, CA when compared to their adjacent normal colorectal epithelial tissues (p < 0.0005, Wilcoxon matched pairs test). Conclusions: This study provided evidence that FZD-3 is involved in CRC carcinogenesis and it is a potential therapeutic target in CRC. No significant financial relationships to disclose.


2005 ◽  
Vol 23 (12) ◽  
pp. 2744-2753 ◽  
Author(s):  
Joseph Kim ◽  
Hiroya Takeuchi ◽  
Stella T. Lam ◽  
Roderick R. Turner ◽  
He-Jing Wang ◽  
...  

Purpose Liver metastasis is the predominant cause of colorectal cancer (CRC) related mortality. Chemokines, soluble factors that orchestrate hematopoetic cell movement, have been implicated in directing cancer metastasis, although their clinical relevance in CRC has not been defined. Our hypothesis was that the chemokine receptor CXCR4 expressed by CRC is a prognostic factor for poor disease outcome. Methods CRC cell lines (n = 6) and tumor specimens (n = 139) from patients with different American Joint Committee on Cancer (AJCC) stages of CRC were assessed. Microarray screening of select specimens and cell lines identified CXCR4 as a prominent chemokine receptor. CXCR4 expression in tumor and benign specimens was assessed by quantitative real-time reverse transcription polymerase chain reaction and correlated with disease recurrence and overall survival. Results High CXCR4 expression in tumor specimens (n = 57) from AJCC stage I/II patients was associated with increased risk for local recurrence and/or distant metastasis (risk ratio, 1.35; 95% CI, 1.09 to 1.68; P = .0065). High CXCR4 expression in primary tumor specimens (n = 35) from AJCC stage IV patients correlated with worse overall median survival (9 months v 23 months; RR, 2.53; 95% CI, 1.19 to 5.40; P = .016). CXCR4 expression was significantly higher in liver metastases (n = 39) compared with primary CRC tumors (n = 100; P < .0001). Conclusion CXCR4, a well-characterized chemokine receptor for T-cells, is differentially expressed in CRC. CXCR4 gene expression in primary CRC demonstrated significant associations with recurrence, survival, and liver metastasis. The CXCR4-CXCL12 signaling mechanism may be clinically relevant for patients with CRC and represents a potential novel target for disease-directed therapy.


Cancers ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 207 ◽  
Author(s):  
Sun-Il Yun ◽  
Hye Kyung Hong ◽  
So-Young Yeo ◽  
Seok-Hyung Kim ◽  
Yong Beom Cho ◽  
...  

Fos-related-antigen-1 (Fra-1), a member of the activator protein-1 (AP-1) transcription factor superfamily, has an essential role in cancer progress and metastasis and Fra-1 is considered a therapeutic target in metastatic cancer including metastatic colorectal cancer (mCRC). However, its regulation at protein level has not yet been clearly elucidated. We found that ubiquitin-specific protease 21 (USP21) increases Fra-1 stability by deubiquitinating Fra-1 and enhances the expression of Fra-1 target genes in colon cancer cells. We also showed that USP21 controlled Fra-1-dependent migration and invasion activities. The oncogenic property of USP21 was confirmed by a significant reduction in liver metastasis when USP21-knockdown cancer cells were injected intrasplenically into mice. Consistently, clinicopathological analysis of colorectal cancer patients revealed a correlation of USP21 expression with high-grade carcinoma and life span. These results demonstrate that USP21 enhances Fra-1 stability and AP-1 target gene expression by deubiquitinating Fra-1. Therefore, USP21 is considered an attractive therapeutic target in mCRC with high Fra-1 expression.


2019 ◽  
Vol 317 (5) ◽  
pp. C869-C880 ◽  
Author(s):  
Marie Lafitte ◽  
Céline Lecointre ◽  
Serge Roche

Metastases remain a major cause of cancer morbidity and mortality. This is a multistep process that involves aberrant cell communication, leading to tumor cell dissemination from the primary tumor and colonization of distinct organs for secondary tumor formation. The mechanisms promoting this pathological process are not fully understood, although they may be of obvious therapeutic interest. Exosomes are small cell-secreted vesicles that contain a large variety of proteins, lipids, and nucleic acids with important signaling activities, and that represent an evolutionarily conserved mechanism for cell-to-cell communication. Not surprisingly, exosome activities have gained strong interest in cancer biology and might play essential roles in metastasis development. Here, we will describe recent findings on the role of exosomes in cancer metastasis formation, particularly in colorectal cancer (CRC). We will also discuss the potential therapeutic value of these vesicles in metastatic cancer.


2021 ◽  
Author(s):  
Mehran Erfani ◽  
Mozhdeh Zamani ◽  
Seyed Younes Hosseini ◽  
Zohreh Mostafavi-Pour ◽  
Sayed Mohammad Shafiee ◽  
...  

Abstract Background Metastasis is a major cause of death in colorectal cancer (CRC) patients, and the epithelial–mesenchymal transition (EMT) has been known to be a crucial event in cancer metastasis. Downregulated expression of AT-rich interaction domain-containing protein 1A (ARID1A), a bona fide tumor suppressor gene, plays an important role in promoting EMT and CRC metastasis, but the underlying molecular mechanisms remain poorly understood. Here, we evaluated the impact of ARID1A knockdown and overexpression on the expression of EMT‑related genes, E-cadherin and β-catenin, in human CRC cells.Methods and Results The expression levels of ARID1A, E-cadherin and β-catenin in CRC cell lines were detected via real-time quantitative PCR (qPCR) and western blot. ARID1A overexpression and shRNA-mediated knockdown were performed to indicate the effect of ARID1A expression on E-cadherin and β-catenin expression in CRC cell lines. The effect of ARID1A knockdown on the migration ability of HCT116 cells was assessed using wound-healing assay. We found that the mRNA and protein expression of adhesive protein E-cadherin was remarkably downregulated in response to shRNA-mediated ARID1A knockdown in HCT116 and HT29 cells. Conversely, overexpression of ARID1A in SW48 cells significantly increased E-cadherin expression. In addition, ARID1A silencing promoted the migration of HCT116 cells. ARID1A knockdown and overexpression did not alter the level of β-catenin expression.Conclusion Our study demonstrates that E-cadherin levels were closely correlated with ARID1A expression. Thus, ARID1A downregulation may promote CRC metastasis through decreasing EMT‑related protein E-cadherin and promoting epithelial cell movement. ARID1A could represent a promising candidate therapeutic target for CRC.


Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 634-634 ◽  
Author(s):  
Flor A. Cianchetti ◽  
Garth W. Tormoen ◽  
Paul E. Bock ◽  
Owen J.T. McCarty

Abstract Abstract 634 Metastatic cancer is associated with a hypercoagulable state, and pathological venous thromboembolic disease is a significant source of morbidity and the second leading cause of death in patients with cancer. Patients with cancer have a 4–10 fold increased risk of developing thrombosis. Recurrent thrombosis can be clinically managed with anticoagulant therapy; however, the risk of bleeding complications associated with the use of anticoagulants has prevented routine prophylactic anticoagulation for patients with cancer who have not yet developed thrombosis. Therefore, a method to identify which cancer patients are at imminent risk to develop thrombosis would allow for an objective means by which to administer personalized anticoagulant prophylaxis, reducing the morbidity and mortality for patients with cancer. There is currently a lack of laboratory assays capable of identifying which patients with cancer are at risk of developing thrombosis. Here we aimed to develop a novel labeling strategy to detect and quantify procoagulant circulating tumor cells (CTCs) from patients with metastatic cancer. We hypothesize that the enumeration of procoagulant CTCs may be prognostic for the development of venous thrombosis in patients with cancer. In this study, we characterized the binding of fluorescently-labeled active site-inhibited factors VIIa, Xa and IIa to the metastatic breast cancer cell line, MDA-MB-231, the non metastatic colorectal cell line, SW480, or the metastatic colorectal cell line, SW620, either in a purified system, in plasma, or in whole blood. Using flow cytometry, labeling of cancer cells in a purified system showed cell and factor-specific characteristics for labeling efficacy. Our data show that a concentration of 50 nM FVIIa-based probe was sufficient to label both the MDA-MB-231 and SW620 cells, while a concentration of 500 nM of the FXa- or FIIa-based probes was required to label both MDA-MB-231 and SW620 cells. A concentration of 0.5 μM FVIIa, 5 μM FXa and 5 μM FIIa was shown to label MDA-MB-231 and SW620 cells in anticoagulated plasma and in plasma under conditions of coagulation. We designed a series of experiments to determine whether our labeling strategy was amenable to a cell processing protocol that utilizes cancer cells being plated onto glass slides. We immobilized MDA-MB-231, SW480, and SW620 cells on functionalized glass surfaces and exposed them to fluorescently labeled FVIIa (0.5 μM), FXa (5 μM), FIIa (10 μM). We found that in a purified system, the MDA-MB-231 cells were robustly labeled with the FVIIa and FXa probes. The FVIIa and FXa probes weakly labeled the SW480 cells and SW620 cells. The FIIa probe failed to label any of the three cell lines. Under conditions of coagulation, the FVIIa probe labeled all the adherent MDA-MB-231 cells. Heterogeneous FVIIa-labeling was observed for both the SW480 and SW620 cell lines, with some of the adherent cells labeling brightly, while other cells on the same slide were not labeled by the FVIIa-probe. The FXa probe showed complete labeling of all three cell lines. The FIIa-probe showed complete labeling of the MDA-MB-231 and SW620 cell lines and heterogeneous labeling of the SW480 cells under conditions of coagulation. In whole blood, the FVIIa probe showed heterogeneous labeling of the MDA-MB-231 cells, SW480 and SW620 cells. Heterogeneous labeling of all three cell lines with the FXa and FIIa probes was observed, with very few SW480 or SW620 cells labeled. All three cell lines were labeled with an anti-TF mAb. In summary, we demonstrated the use of fluorescently-modified, active site-inhibited coagulation factors to label procoagulant cancer cells. We demonstrated that coagulation factors based-probes bound to cancer cell lines in purified systems and in whole blood, yet failed to bind to peripheral blood cells. Labeling of cancer cells was demonstrated via flow cytometry in purified systems, as well as on an immobilized-cell platform similar to what is currently used in some CTC-detection platforms. This work is the first step in the development of a function-based CTC labeling strategy to determine whether CTCs are procoagulant, and whether CTC enumeration and procoagulant characterization strategies are clinically useful in predicting thrombosis in patients with cancer. Disclosures: No relevant conflicts of interest to declare.


Sign in / Sign up

Export Citation Format

Share Document