Construction of key signal regulatory network in metastatic colorectal cancer

The role of miR-4469 as a tumor suppressor regulating inflammatory cell infiltration in colorectal cancer

Background

MicroRNA (miRNA) regulates gene expression posttranscriptionally, and some of them function in tumor suppression and can be used in drug development. As a result, identifying and screening miRNAs that suppress tumors would be a significant addition to tumor treatment.

Methods

In this study, we analyzed the miRNA expression profile of colorectal cancer (CRC), constructed a negative regulatory network of the miRNA-target genes, and identified miR-4469 as one of the key tumor suppressors miRNAs. We analyzed the expression and survival of miR-4469 in pan-cancer, experimentally verified the expression level of miR-4469 in CRC cells and the effect on CRC cell proliferation and migration. We screened miR-4469 target genes for enrichment analysis and immune cell infiltration analysis and validated target gene expression to clarify the regulatory mechanisms involved in miR-4469.

Results

miR-4469 was more highly expressed in normal colorectum tissues compared to CRC tissues and correlated with survival time in patients with multiple cancers. It was shown that miR-4469 was highly expressed in normal colon cells and miR-4469 expression could inhibit the proliferation and migration of CRC cells. In addition, studies on the mechanism showed that miR-4469 function is mainly related to the regulation of inflammatory cell infiltration, and the key target genes of miR-4469 in this process are SLC2A3, FGR, PLEKHO2, and MYO1F.

Conclusion

miR-4469 is a tumor suppressor in CRC, and its regulatory mechanism mainly affects the infiltration of inflammatory cells in the cancer tissue.

A network pharmacology-based investigation on the bioactive ingredients and molecular mechanisms of Gelsemium elegans Benth against colorectal cancer

BACKGROUND

Colorectal cancer (CRC) remains one of the leading causes of cancer-related death worldwide. Gelsemium elegans Benth (GEB) is a traditional Chinese medicine commonly used for treatment for gastrointestinal cancer, including CRC. However, the underlying active ingredients and mechanism remain unknown. This study aims to explore the active components and the functional mechanisms of GEB in treating CRC by network pharmacology-based approaches.

METHODS

Candidate compounds of GEB were collected from the Traditional Chinese Medicine@Taiwan, Traditional Chinese Medicines Integrated Database, Bioinformatics Analysis Tool for Molecular mechanism of Traditional Chinese Medicine, and published literature. Potentially active targets of compounds in GEB were retrieved from SwissTargetPrediction databases. Keywords "colorectal cancer", "rectal cancer" and "colon cancer" were used as keywords to search for related targets of CRC from the GeneCards database, then the overlapped targets of compounds and CRC were further intersected with CRC related genes from the TCGA database. The Cytoscape was applied to construct a graph of visualized compound-target and pathway networks. Protein-protein interaction networks were constructed by using STRING database. The DAVID tool was applied to carry out Gene Ontology and Kyoto Encyclopedia of Genes and Genome pathway enrichment analysis of final targets. Molecular docking was employed to validate the interaction between compounds and targets. AutoDockTools was used to construct docking grid box for each target. Docking and molecular dynamics simulation were performed by Autodock Vina and Gromacs software, respectively.

RESULTS

Fifty-three bioactive compounds were successfully identified, corresponding to 136 targets that were screened out for the treatment of CRC. Functional enrichment analysis suggested that GEB exerted its pharmacological effects against CRC via modulating multiple pathways, such as pathways in cancer, cell cycle, and colorectal cancer. Molecular docking analysis showed that the representative compounds had good affinity with the key targets. Molecular dynamics simulation indicated that the best hit molecules formed a stable protein-ligand complex.

CONCLUSION

This network pharmacology study revealed the multiple ingredients, targets, and pathways synergistically involved in the anti-CRC effect of GEB, which will enhance our understanding of the potential molecular mechanism of GEB in treatment for CRC and lay a foundation for further experimental research.

A newly identified small molecular compound acts as a protein kinase inhibitor to suppress metastasis of colorectal cancer

BACKGROUND

Targeted therapy has demonstrated high efficacy in the treatment of advanced cancer, and protein kinase inhibitors are a major focus of that therapy; therefore, our study aimed to identify a new protein kinase inhibitor that could be used in the treatment of advanced cancers.

METHODS

We analyzed the expression profile of colorectal cancer (CRC), combined the driver gene and drug target databases, and identified protein kinase kalirin RhoGEF kinase (kalirin/KALRN) which is related to CRC metastasis. Based on the structure of kalirin, we screened for the small molecular compound ZINC65387069. We first compared the kinase inhibitory activities and molecular properties of ZINC65387069 and tyrosine kinase inhibitors (TKIs). We then determined the effects of ZINC65387069 on the phosphorylation of protein kinase B-Raf. Finally, we determined the effects of ZINC65387069 on migration and apoptosis of HCT116 cells as well as RKO cells. The cell cytoskeleton was also determined.

RESULTS

Compared with traditional TKIs, ZINC65387069 had stronger kinase inhibitory activity, a simpler structure, higher water solubility, a smaller polar surface area, and lower molecular weight and volume. In CRC cells, ZINC65387069 could significantly inhibit the phosphorylation of B-Raf as well as inhibit cell migration, destroy the cell cytoskeleton, and promote cell apoptosis.

CONCLUSION

ZINC65387069 is a newly identified protein kinase inhibitor that deserves additional research as a lead compound for drug development to help create targeted therapy against CRC.

The inhibition of colorectal cancer growth by the natural product macrocarpal I

BACKGROUND

Presently, few small molecule compounds are used as targeted therapy drugs in the treatment of colorectal cancer (CRC). It is important to identify new small molecule compounds, which can be used in the treatment of CRC.

METHODS

In this study, we selected four protein molecules as drug targets: PRL-3 (Phosphatase of regenerating liver 3), CLIC4 (Chloride intracellular channel 4), THBS2 (Thrombospondin 2), and BGN (Biglycan). These protein molecules were associated with the growth and metastasis of CRC cells. Small molecular compounds were screened on the basis of their target structures. Thus, five small molecule compounds were screened from each target structure, and three small molecule compounds (macrocarpal I, sildenafil, and neoandrographolide) were found to bind with two drug targets at the same time. Further experiments revealed that the inhibition rate of macrocarpal I was the highest in CRC cells. Therefore, we determined the effects of macrocarpal I on proliferation, apoptosis, cytoskeleton of CRC cells, and subcutaneous tumorigenesis in nude mice. Furthermore, RNA-seq analysis was performed to determine the molecular mechanism through which macrocarpal I inhibited the progression of CRC.

RESULTS

We found that macrocarpal I could effectively inhibit proliferation, colony formation of CRC cells, and subcutaneous tumorigenesis in nude mice. Moreover, it also destroyed the cytoskeleton of CRC cells and promoted apoptosis. The effects on kinase activity, cytoskeleton, and DNA repair is the mechanism of macrocarpal I to inhibiting CRC growth.

CONCLUSION

Macrocarpal I is a small molecule compound that can effectively inhibit the progression of CRC. Thus, macrocarpal I is a therapeutic compound that shows promising results in the treatment of advanced CRC.

Atractyloside targets cancer-associated fibroblasts and inhibits the metastasis of colon cancer

Background

Several evidences have proved that cancer-associated fibroblasts (CAFs) play a crucial role in tumor progression. In fact, CAFs form a major component of tumor microenvironment (TME). Therefore, the development and metastasis of tumors can be effectively inhibited by small molecular compounds that target CAFs.

Methods

In this study, we mainly analyzed the expression profile of colon cancer (CC). We determined the intensity of CAFs in CC tissues by using the immune cell infiltration score. Gene enrichment analysis and the screening of differentially expressed genes were performed on the basis of the intensity of CAFs in CC tissues. We screened the small molecular compounds that were converted from differentially expressed genes. The results indicated that atractyloside was a small molecular compound related to CAFs in CC tissues. We identified the relationship between atractylosides and CAFs through target protein analysis and network analysis, and verified the inhibition effect of atractylosides on CC cells (CCC) by migration assay and scratch wound-healing assays.

Results

We found that many target proteins of atractyloside, such as the matrix metalloproteinase family and integrin proteins, were related to the biological function of CAFs. By performing network analysis, we found that the target proteins FGF1, ITGB1, and EDNRA were closely related to tumor angiogenesis, while the target proteins MMP9 and ITGAV were correlated to an extracellular matrix (ECM) and cell motility. These findings which further confirmed the relationship between atractylosides and CAFs. In addition, transwell cell migration and scratch wound-healing assays proved that atractylosides could significantly inhibit the migration of CCCs.

Conclusions

The atractyloside might be a small molecular compound that potentially targets CAFs and inhibits the development as well as metastasis of CC by changing the TME.

Eotaxins and Their Receptor in Colorectal Cancer-A Literature Review

Colorectal cancer (CRC) is one of the most common malignancies in the world, with a global incidence of almost 2 million new cases every year. Despite the availability of many diagnostic tests, including laboratory tests and molecular diagnostics, an increasing number of new cases is observed. Thus, it is very important to search new markers that would show high diagnostic sensitivity and specificity in the detection of colorectal cancer in early stages of the disease. Eotaxins are proteins that belong to the cytokine group-small molecules with a variety of applications. Their main role is the activation of basophils and eosinophils involved in inflammatory processes. Therefore, we performed an extensive search of the literature pertaining to our investigation via the MEDLINE/PubMed database. On the basis of available literature, we can assume that eotaxins accumulate in cancer cells in the course of CRC. This leads to a decrease in the chemotaxis of eosinophils, which are effector immune cells with anti-tumor activity. This may explain a decrease in their number as a defense mechanism of cancer cells against their destruction and may be useful when attempting anti-tumor therapy with the use of chemokines.

Effect of glucose deprivation on the expression of genes encoding glucocorticoid receptor and some related factors in ERN1-knockdown U87 glioma cells

OBJECTIVE

The aim of the present study was to examine the effect of glucose deprivation on the expression of genes encoded glucocorticoid receptor (NR3C1) and some related proteins (NR3C2, AHR, NRIP1, NNT, ARHGAP35, SGK1, and SGK3) in U87 glioma cells in response to inhibition of endoplasmic reticulum stress signaling mediated by ERN1/IRE1 (endoplasmic reticulum to nucleus signaling 1/inositol requiring enzyme 1) for evaluation of their possible significance in the control of glioma growth through endoplasmic reticulum stress signaling mediated by IRE1 and glucose deprivation.

METHODS

The expression of NR3C1, NR3C2, AHR, NRIP1, NNT, ARHGAP35, SGK1, and SGK3 genes in U87 glioma cells transfected by empty vector pcDNA3.1 (control cells) and cells without ERN1 signaling enzyme function (transfected by dnERN1) under glucose deprivation was studied by real time quantitative polymerase chain reaction.

RESULTS

It was shown that the expression level of NR3C2, AHR, SGK1, SGK3, and NNT genes was up-regulated in control U87 glioma cells under glucose deprivation condition in comparison with the control cells growing with glucose. At the same time, the expression of NRIP1 gene is down-regulated in these glioma cells under glucose deprivation, but NR3C1 and ARHGAP35 genes was resistant to this experimental condition. We also showed that inhibition of ERN1 signaling enzyme function significantly modified the response of most studied gene expressions to glucose deprivation condition. Thus, effect of glucose deprivation on the expression level of NR3C2, AHR, and SGK1 genes was significantly stronger in ERN1 knockdown U87 glioma cells since the expression of NNT gene was resistant to glucose deprivation condition. Moreover, the inhibition of ERN1 enzymatic activities in U87 glioma cells led to up-regulation of ARHGAP35 gene expression and significant down-regulation of the expression of SGK3 gene in response to glucose deprivation condition.

CONCLUSIONS

Results of this study demonstrated that glucose deprivation did not change the expression level of NR3C1 gene but it significantly affected the expression of NR3C2, AHR, NRIP, SGK1, SGK3, and NNT genes in vector-transfected U87 glioma cells in gene specific manner and possibly contributed to the control of glioma growth since the expression of most studied genes in glucose deprivation condition was significantly dependent on the functional activity of IRE1 signaling enzyme.

Application of weighted gene co‑expression network analysis to explore the potential diagnostic biomarkers for colorectal cancer

Colorectal cancer (CRC) is one of the most common malignant diseases in the world. Although mechanistic studies have been conducted on the pathogenesis of CRC, the molecular mechanism of CRC tumorigenesis remains unclear. In the present study, the weighted gene co-expression network analysis was performed for the Gene Expression Omnibus (GEO) dataset GSE87211, in order to analyze the key modules involved in the pathogenesis of CRC. Next, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed on the key module genes to analyze the functional pathways involved. The hub genes were screened using the Cytoscape platform and verified by a second GEO dataset, GSE21510. Finally, 10 hub genes were identified in 2 key modules (the green and brown modules) as the genes most significantly associated with the tumorigenesis of CRC. The 5 hub genes from the green module included collagen type I α1 chain, collagen type XII α1 chain, collagen triple helix repeat containing 1, inhibin subunit βa (INHBA) and chromobox 2 (CBX2), while the 5 hub genes from the brown module included bestrophin 2 (BEST2), carbonic anhydrase 2, glucagon, solute carrier family 4 member 4 and gliomedin. The 2 key modules with the 10 hub genes identified may regulate the occurrence and development of CRC through the extracellular matrix pathway, PI3K-Akt and chemokine signaling pathways, thus providing a reference for understanding the complex mechanism of tumorigenesis in CRC. Of note, few studies have reported the pathogenesis of CRC with the 3 identified hub genes, INHBA, CBX2 and BEST2. Further investigation of the molecular mechanism of these genes in CRC is recommended.

Regulatory Mechanism of ITGBL1 in the Metastasis of Colorectal Cancer

Integrin, beta-like 1 (ITGBL1) protein is located in the extracellular matrix (ECM) and involved in the development and metastasis of many tumors. However, the regulatory mechanism of ITGBL1 in colorectal cancer (CRC) remains unclear. This study was to analyze the expression profile of CRC and to identify the expression change of ITGBL1 gene at different stages of CRC. Survival analysis showed that ITGBL1 was related to the metastasis of CRC, and CRC patients with a high expression of ITGBL1 had earlier metastasis. Gene Set Enrichment Analysis (GSEA) indicated the relationship between ITGBL1 expression and molecular events of CRC. The results indicated that a high expression of ITGBL1 was linked to Wnt signaling pathway, cell polarity, and tissue development, while a low expression of ITGBL1 was related to cellular respiration, electron transfer chain, and oxidative phosphorylation. With the expression profiles from interstitial and parenchyma CRC tissues, a comparison was made to determine the difference between high/low expression of ITGBL1 and Wnt signaling pathway, respectively, and further confirmed the close relation between ITGBL1 and Wnt signaling pathway. To determine the relation, an interaction network of ITGBL1 and Wnt signaling proteins was constructed. It was found that β-catenin interacted with multiple extracellular Wnt signals and could bind to ITGBL1. As a result, the regulatory mechanism of ITGBL1 in CRC is related to extracellular Wnt signals and may affect extracellular Wnt signals via β-catenin.

IPO5 promotes the proliferation and tumourigenicity of colorectal cancer cells by mediating RASAL2 nuclear transportation

Background

Karyopherin nuclear transport receptors play important roles in tumour development and drug resistance and have been reported as potential biomarkers and therapeutic targets for tumour treatment. However, IPO5, one of the karyopherin nuclear transport receptor family members, remains largely uncharacterized in tumour progression.

Methods

The TCGA data, quantitative reverse transcription-PCR (qRT-PCR), western blotting, and IHC analyses were used to detect IPO5 expression in CRC tissues. A series of in vivo and in vitro experiments was utilized to demonstrate the function of IPO5 in CRC tissues. Mass spectrometry (MS), CO-IP technology, subcellular fractionation, and immunofluorescence were utilized to investigate the possible mechanisms of CRC.

Results

IPO5 was highly expressed and positively correlated with the clinicopathological characteristics of colorectal cancer tissues. Functional experiments indicated that IPO5 could promote the development of CRC. Mechanistically, we screened RASAL2, one cargo of IPO5, and further confirmed that IPO5 bound to the NLS sequence of RASAL2, mediating RASAL2 nuclear translocation and inducing RAS signal activation, thereby promoting the progression of CRC.

Conclusions

Together, our results indicate that IPO5 is overexpressed in colorectal cancer cells. By transporting RASAL2, IPO5 may play a crucial role in CRC.

Electronic supplementary material

The online version of this article (10.1186/s13046-019-1290-0) contains supplementary material, which is available to authorized users.

TNK2 as a key drug target for the treatment of metastatic colorectal cancer

Currently, few small molecular compounds are being used as therapeutic targets in the treatment of metastatic colorectal cancer (CRC); therefore, there is an urgent need to identify novel drug targets, which could be used in the treatment of CRC. The Connectivity Map (cmap) web server was used to correlate the differentially expressed genes of CRC with the small molecular compounds related to the disease. Thus, we identified six small molecular compounds to be potentially relevant to the development of CRC. Target protein analysis revealed that TNK2 is a common target of the three small molecular compounds, which were included in the set of six small molecular compounds mentioned earlier. In addition, the continuous activation of TNK2 was observed in the development of CRC. This indicates that TNK2 may have the potential of being a key drug target in the treatment of metastatic CRC. The Molinspiration tool was used to analyze small molecular compounds, which are bound to TNK2 in the Protein Data Bank (PDB). We found that a small molecular compound in protein with the PDB identification code 4EWH had higher scores in terms of kinase inhibition but lower scores in terms of other biological activity indices. This indicates that the compound had good kinase specificity, which is a key characteristic of other existing clinically approved anti-tumor small molecular compounds. By performing target protein prediction analysis, we identified 122 target proteins of the small molecular compound in 4EWH. Out of the 122 target proteins, 21 proteins showed kinase activity, including TNK2. Enrichment analysis was performed on the diseases in which these 122 target proteins were involved, and the results revealed that CRC had the highest correlation. Moreover, 47 target proteins were individually correlated with the progression of CRC. This further suggests that the small molecular compound can inhibit CRC. Thus, TNK2 was considered as a potential drug target in the treatment of metastatic CRC.