Stability of matrix metalloproteinase-9 as biological marker in colorectal cancer

Integrated bioinformatics approach to unwind key genes and pathways involved in colorectal cancer

BACKGROUND

Colorectal cancer (CRC) is the fifth leading cause of death in India. Until now, the exact pathogenesis concerning CRC signaling pathways is largely unknown; however, the diseased condition is believed to deteriorate with lifestyle, aging, and inherited genetic disorders. Hence, the identification of hub genes and therapeutic targets is of great importance for disease monitoring.

OBJECTIVE

Identification of hub genes and targets for identification of candidate hub genes for CRC diagnosis and monitoring.

MATERIALS AND METHODS

The present study applied gene expression analysis by integrating two profile datasets (GSE20916 and GSE33113) from NCBI-GEO database to elucidate the potential key candidate genes and pathways in CRC. Differentially expressed genes (DEGs) between CRC (195 CRC tissues) and healthy control (46 normal mucosal tissue) were sorted using GEO2R tool. Further, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis were performed using Cluster Profiler in Rv. 3.6.1. Moreover, protein-protein interactions (PPI), module detection, and hub gene identification were accomplished and visualized through the Search Tool for the Retrieval of Interacting Genes, Molecular Complex Detection (MCODE) plug-in of Cytoscape v3.8.0. Further hub genes were imported into ToppGene webserver for pathway analysis and prognostic expression analysis was conducted using Gene Expression Profiling Interactive Analysis webserver.

RESULTS

A total of 2221 DEGs, including 1286 up-regulated and 935down-regulated genes mainly enriched in signaling pathways of NOD-like receptor, FoxO, AMPK signalling and leishmaniasis. Three key modules were detected from PPI network using MCODE. Besides, top 20 high prioritized hub genes were selected. Further, prognostic expression analysis revealed ten of the hub genes, namely IL1B, CD44, Glyceraldehyde-3-phosphate dehydrogenase (GAPDH, MMP9, CREB1, STAT1, vascular endothelial growth factor (VEGFA), CDC5 L, Ataxia-telangiectasia mutated (ATM + and CDH1 to be differently expressed in normal and cancer patients.

CONCLUSION

The present study proposed five novel therapeutic targets, i.e., ATM, GAPDH, CREB1, VEGFA, and CDH1 genes that might provide new insights into molecular oncogenesis of CRC.

Perivascular mast cells and expression of vascular endothelial growth factor, laminin-332 and matrix metalloproteinase-9 in human colorectal neoplasms

INTRODUCTION AND AIMS

Colorectal cancer (CRC) is one of the most prevalent cancers worldwide, and significantly contributes to cancer-related deaths. Most cases arise from adenomatous polyps. Biomarkers currently play an important role in tumor progression. Our aim was to identify perivascular mast cells and analyze the expression of laminin-332, MMP-9, and VEGF in cases of adenoma and CRC in humans.

MATERIALS AND METHODS

Patients were selected at the Coloproctology Service and samples were obtained through biopsies. Adenoma and CRC slides were examined, utilizing immunohistochemistry to detect molecules, and were processed, using 1% Alcian Blue (pH 0.5) for mast cell staining.

RESULTS

Higher density of perivascular mast cells was observed in adenomas. Laminin-332 expression revealed basement membrane discontinuity associated with tumor invasion in CRC. MMP-9 immunostaining in adenoma was detected in glandular epithelium and lining epithelium, in areas close to the basement membrane, whereas in CRC, the enzyme was found in the cytoplasm of invasive clusters. VEGF expression was associated with cell atypia in adenoma and in areas of disorganization of the epithelium-connective tissue interface in CRC. VEGF has also been detected in endothelial cells from microvessels.

CONCLUSIONS

We demonstrated the different patterns of perivascular mast cells and molecular expression in colorectal neoplasms. Those analyses favor the recognition of the predisposition to the disease, or its early stage, and have the potential to define the molecular profile of the lesions.

Stage-Dependent Levels of Brain-Derived Neurotrophic Factor and Matrix Metalloproteinase 9 in the Prognosis of Colorectal Cancer

PURPOSE

The development of sensitive and non-invasive biomarkers for the early detection of CRC and determination of their role in the individual stages of CRC.

METHODS

MMP-9 expression in serum and tissue, and BDNF expression in plasma were detected using the ELISA method. MMP-9 and BDNF in the tissue were also determined by immunohistochemical staining.

RESULTS

To assess the balance between changes in survival and tumor progression, we compared BDNF/MMP-9 ratios in tissues of living and deceased individuals. The tissue BDNF/MMP-9 ratio (evaluated immunohistochemically) decreased significantly with the progression of the disease in living patients. The BDNF/MMP-9 ratio was statistically significantly reduced in stages II and III compared to the benign group. However, in deceased individuals, the ratio showed an opposite tendency.

CONCLUSION

The determination of the tissue BDNF/MMP9 ratio can be used as a prognostic biomarker of CRC.

Mechanism of remodeling and local effects in vivo of a new injectable cosmetic filler

By studying the local effects of a new type of injectable cosmetic filler implanted into the animal to explore the mechanism of remodeling and cosmetic effect of this kind of product. Take 12 rabbits and select 4 implantation points on both sides of the spine, respectively, and implant the test sample (PLLA) and negative control sample (HDPE) into the subcutaneous tissues on both sides. In the same way, take another 12 rabbits and implant the marketing control sample (cross-linked sodium hyaluronate) and negative control sample (HDPE) into the subcutaneous tissues on both sides. The animals were executed at 1 week, 4 weeks, 13 weeks and 52 weeks respectively, and Hematoxylin-Eosin staining, Masson trichrome staining and immunofluorescence staining were performed to characterize the local effects in vivo and the expression of type I collagen (Col. I), type III collagen (Col.III) and matrix metalloproteinase 9 (MMP-9). Good histocompatibility of the test sample and the marketing control sample were found. The foreign body reaction of marketing control sample was more intense than that of the test sample after 13 weeks. The foreign body reaction of testing sample was more intense after 52 weeks, while that of the marketing control sample was more stable. With the process of tissue repair, the collagen fibers of test samples and marketing control samples gradually increased after implantation. Type I collagen was mainly found inside the fiber capsule, while type III collagen was mainly found outside. The positive expression of matrix metalloproteinase 9 gradually increased, the positive expression of test samples increased significantly after 52 weeks, while that of marketing control samples did not change significantly. Good histocompatibility of PLLA filler is found. Matrix metalloproteinase 9 participates in foreign body reaction and collagen formation, which can reflect the process of tissue remodeling.

Overexpression of miRNA 26a and 26b with MMP-9 are valuable diagnostic biomarkers for colorectal cancer patients

Background: The key role of miRNA expression in incidence and progression of colorectal cancer (CLC) have been developed over the last decade. Materials & methods: A total of 153 subjects were enrolled into two phases: 14 selected miRNAs were first evaluated in 50 subjects, then miR-26a and miR-26b relative expression were further evaluated in 103 subjects and their target protein MMP-9 was measured. Results: miR-26a and -26b showed highly significant overexpression. Both miR-26a and -26b (p < 0.001) had high diagnostic efficacy for CRC. There was a significant increase in serum MMP-9 protein in CRC patients with positive correlation with miR-26a and -26b expression levels (p < 0.001). Conclusion: miRNA 26a and 26b with MMP-9 can be used as diagnostic biomarker for CRC patients.

Alterations of the Extracellular Matrix in Colorectal Carcinoma

Background: The process of proliferation and invasion of tumor cells depends on changes in the extracellular matrix (ECM) through the activation of enzymes and alterations in the profile of ECM components. Our aims are to investigate the mRNA and protein expression profiles of the ECM components, heparanase-1 (HPSE), heparanase-2 (HPSE2), matrix metalloproteinase-9 (MMP-9), and syndecan-1 (SDC1) in neoplastic and nonneoplastic tissues of 24 patients with colorectal carcinoma (CRC) and to test for associations between these expression patterns with the presence or absence of lymph node metastasis. Materials and Methods: This was a cross-sectional study in which 24 adult patients with CRC were admitted for resectional surgery. We analyzed the mRNA and protein expression patterns of the HPSE, HPSE2, MMP-9, and SDC1 genes by quantitative reverse transcription PCR and immunohistochemistry, respectively. Additionally, we investigated whether variations exist in the expression of the ECM components between the affected tissue and nontumoral tissue collected from the same patient. Tissue samples were collected immediately after the surgical resection. Results and Conclusion: The data showed higher mRNA and protein expression levels of HPSE2 (p = 0.0058), MMP-9 (p = 0.0268), and SDC1 (p = 0.0002) in tumor samples when compared with the nonneoplastic tissues. There was, however, only an increase in the level of the HPSE protein in the tumoral tissues. Increased expression of HPSE2 was observed in patients with lymph node metastasis (p = 0.031). This elevation in HPSE2 mRNA expression in patients with lymph node metastasis potentially indicates that it may participate in driving colorectal carcinoma progression.

A network-based pharmacological investigation to identify the mechanistic regulatory pathway of andrographolide against colorectal cancer

Traditional cancer treatments have posed numerous obstacles, including toxicity, multiple drug resistance, and financial cost. On the contrary, bioactive phytochemicals used in complementary alternative medicine have recently increased attention due to their potential to modulate a wide range of molecular mechanisms with a less toxic effect. Therefore, we investigated the potential regulatory mechanisms of andrographolide to treat colorectal cancer (CRC) using a network pharmacology approach. Target genes of andrographolide were retrieved from public databases (PharmMapper, Swiss target prediction, Targetnet, STITCH, and SuperPred), while targets related to CRC were retrieved from disease databases (Genecards and DisGeNet) and expression datasets (GSE32323 and GSE8671) were retrieved from gene expression omnibus (GEO). Protein-protein interaction networks (PPI) were generated using STRING and Cytoscape, and hub genes were identified by topology analysis and MCODE. Annotation of target proteins was performed using Gene Ontology (GO) database DAVID and signaling pathway enrichment analysis using the Kyoto Encyclopedia and Genome Database (KEGG). Survival and molecular docking analysis for the hub genes revealed three genes (PDGFRA, PTGS2, and MMP9) were involved in the overall survival of CRC patients, and the top three genes with the lowest binding energy include PDGFRA, MET, and MAPK1. MET gene upregulation and PDGFRA and PTGS2 gene downregulation are associated with the survival of CRC patients, as revealed by box plots and correlation analysis. In conclusion, this study has provided the first scientific evidence to support the use of andrographolide to inhibit cellular proliferation, migration, and growth, and induce apoptosis by targeting the hub genes (PDGFRA, PTGS2, MMP9, MAPK1, and MET) involved in CRC migration and invasion.

Plasma MMP-1 Expression as a Prognostic Factor in Colon Cancer

BACKGROUND

Matrix metalloproteinases (MMP) are involved in the local and distant invasiveness of colorectal cancer. This study investigates the prognostic value of circulating matrix metalloproteinase levels in patients with colon cancer.

METHODS

A cohort of 152 patients was followed for more than 10 years. The correlation of plasma levels of MMP-1,-2, -7, -8, and -9 and survival was investigated.

RESULTS

A high level of MMP-1 in circulating plasma was associated with a poorer prognosis in colon cancer (HR 2.0, 95% CI 1.1-3.9) in multivariate analysis regarding 5-year cancer-specific survival. This was further seen in regard of 10-year cancer-specific survival.

CONCLUSIONS

Measurement of plasma MMP-1 concentration in patients planned for radical colon cancer surgery might be of importance when discussing prognosis and selection of patients for oncological treatment and postsurgery surveillance.

Matrix metalloproteinase-2, -7, and -9 activities in dogs with idiopathic pulmonary fibrosis compared to healthy dogs and dogs with other respiratory diseases

BACKGROUND

Canine idiopathic pulmonary fibrosis (CIPF) is a chronic, interstitial lung disease that mainly affects West Highland white terriers (WHWTs) and is characterized by excessive deposition of extracellular matrix (ECM) in the lung. Matrix metalloproteinases (MMPs) participate in remodeling of ECM.

OBJECTIVES

To compare metalloproteinase-2, -7 and -9 activities in blood or bronchoalveolar lavage fluid (BALF) samples or both of CIPF WHWTs with healthy WHWTs, healthy dogs of other breeds, and dogs with other lung diseases and determine if these MMPs could be used as diagnostic and prognostic markers for CIPF.

ANIMALS

Forty-four CIPF WHWTs, 24 dogs with chronic bronchitis (CB), 17 with eosinophilic bronchopneumopathy (EBP), 10 with bacterial pneumonia, 39 healthy WHWTs, and 35 healthy dogs of other breeds.

METHODS

Cross-sectional observational study. Pro-MMP and active MMP activities were analyzed by zymography.

RESULTS

In serum, significantly higher (P < .01) pro-MMP-7 activities were observed in CIPF WHWTs compared to healthy dogs of other breeds, dogs with CB and dogs with EBP. In BALF of CIPF WHWTs, both pro-MMP-9 and pro-MMP-2 activities were significantly higher (P < .01) compared to healthy WHWTs, but these differences were not detected in plasma. The CIPF WHWTs had significantly higher (P < .05) activities of pro-MMP-9 compared to dogs with CB and of pro-MMP-2 compared to dogs with CB and EBP. No statistically significant prognostic factors were observed in CIPF WHWTs.

CONCLUSIONS AND CLINICAL RELEVANCE

Serum MMP-7 and BALF MMP-2 and -9 potentially may be useful diagnostic markers but not prognostic markers for CIPF.

Promising targets of chrysin and daidzein in colorectal cancer: Amphiregulin, CXCL1, and MMP-9

Colorectal cancer is one of the primary causes of cancer-related mortality worldwide. The tumor microenvironment contains growth factors; inflammatory chemokines, matrix metalloproteinases, and pro-oxidants leading to cancer development and progression. Phytochemicals have been used as the main source of anti-cancer agents. Accordingly, the effect of two natural flavonoids (Chrysin and Daidzein) was investigated on the level of amphiregulin (AREG), chemokine ligand (CXCL1), and matrix metalloproteinase-9 (MMP-9) in 1, 2-dimethylhydrazine dihydrochloride (DMH) induced colorectal cancer. Rats were injected by DMH (40 mg/kg/week S.C.) for 16 weeks concomitantly with 2% dextran sodium sulfate (DSS) in drinking water for three cycles. Rats were orally treated with chrysin (125 and 250 mg/kg) and daidzein (5 and10 mg/kg) three times/week for the last 8 weeks. DMH + DSS group showed a significant (P < 0.05) increase in the levels of AREG (2386 ± 18 vs 1377 ± 10 pg/ml), CXCL1 (18 ± 0.9 vs 6 ± 0.83 <mu>g/ml), MMP-9 (1355 ± 88 vs 452 ± 7 pg/ml) compared to normal rats. These findings were associated with a potent antioxidant activity against cytochrome P450 2E1; (CYP2E1). Histopathological findings of the DMH + DSS group showed focal hyperplasia of the mucosa lining overlying crypts with moderate inflammation, dysplastic epithelial cells, and loss of goblet cells. Chrysin and daidzein treatment significantly (P < 0.05) restored the biochemical alterations and reverted histopathological findings near to the normal status. Moreover, chrysin and daidzein exerted anticancer activity against SW620 cells that were associated with decreased the protein expression of p-ERK/ERK and p-AKT/AKT. In conclusion, this study highlighted the potential anticancer role of chrysin and daidzein in the treatment of colon cancer.

6-Gingerol delays tumorigenesis in benzo[a]pyrene and dextran sulphate sodium-induced colorectal cancer in mice

Colorectal cancer (CRC) has been linked to dietary consumption of benzo[a]pyrene (B[a]P). 6-Gingerol (6-G), a component of ginger has been reported to possess anti-inflammatory and antioxidant activities, but little is known regarding the mechanism of 6-G in CRC chemoprevention. We therefore investigated the effect of 6-G on B[a]P. and dextran sulphate sodium (DSS) induced CRC in mice. Mice in Group I and Group II received corn oil and 6-G orally at 2 ml/kg and 100 mg/kg, respectively for 126 days. Group III were administered 125 mg/kg of B[a]P for 5 days followed by 3 cycles of 4% dextran sulphate sodium (DSS). Group IV received 6-G for 7 days followed by co-administration with 125 mg/kg of B[a]P. for 5 days and 3 cycles of 4% DSS. Tumor formation was reduced and expression of Ki-67, WNT3a, DVL-2 and β-catenin following 6-G exposure. Also, 6-G increases expression of APC, P53, TUNEL positive nuclei and subsequently decreased the expression of TNF-α, IL-1β, INOS, COX-2 and cyclin D1. 6-G inhibited angiogenesis by decreasing the concentration of VEGF, Angiopoietin-1, FGF and GDF-15 in the colon of B[a]P. and DSS exposed mice. Overall, 6-G attenuated B[a]P and DSS-induced CRC in mice via anti-inflammatory, anti-proliferative and apoptotic mechanisms.

PathME: pathway based multi-modal sparse autoencoders for clustering of patient-level multi-omics data

Background

Recent years have witnessed an increasing interest in multi-omics data, because these data allow for better understanding complex diseases such as cancer on a molecular system level. In addition, multi-omics data increase the chance to robustly identify molecular patient sub-groups and hence open the door towards a better personalized treatment of diseases. Several methods have been proposed for unsupervised clustering of multi-omics data. However, a number of challenges remain, such as the magnitude of features and the large difference in dimensionality across different omics data sources.

Results

We propose a multi-modal sparse denoising autoencoder framework coupled with sparse non-negative matrix factorization to robustly cluster patients based on multi-omics data. The proposed model specifically leverages pathway information to effectively reduce the dimensionality of omics data into a pathway and patient specific score profile. In consequence, our method allows us to understand, which pathway is a feature of which particular patient cluster. Moreover, recently proposed machine learning techniques allow us to disentangle the specific impact of each individual omics feature on a pathway score. We applied our method to cluster patients in several cancer datasets using gene expression, miRNA expression, DNA methylation and CNVs, demonstrating the possibility to obtain biologically plausible disease subtypes characterized by specific molecular features. Comparison against several competing methods showed a competitive clustering performance. In addition, post-hoc analysis of somatic mutations and clinical data provided supporting evidence and interpretation of the identified clusters.

Conclusions

Our suggested multi-modal sparse denoising autoencoder approach allows for an effective and interpretable integration of multi-omics data on pathway level while addressing the high dimensional character of omics data. Patient specific pathway score profiles derived from our model allow for a robust identification of disease subgroups.

Enhanced SLP-2 promotes invasion and metastasis by regulating Wnt/β-catenin signal pathway in colorectal cancer and predicts poor prognosis

Stomatin-like protein-2 (SLP-2) gene belongs to the stomatin supergene family, and previous studies have revealed up-regulated SLP-2 expression in gallbladder cancer, lung cancer, and esophageal cancer, while the role of SLP-2 in colorectal cancer (CRC) remains unclear and needs further investigation. Therefore, the expression levels of SLP-2 in CRC tissue and cell lines were tested in this study. Besides, we further explored the role of SLP-2 in CRC invasion and metastasis at molecular level via gene intervention technique. Our results demonstrated that the positive rate of SLP-2 expression in CRC tissues was higher than that in the adjacent non-cancerous tissues (P < 0.05); positive SLP-2 expression predicted poorer prognosis of CRC patients as an independent risk factor (P < 0.05). Cell activities and the capacity of migration and invasion significantly decreased after the suppression of SLP-2 in SW620 cells (P < 0.05). Furthermore, the suppression of SLP-2 in SW620 cells resulted in varieties of invasion and metastasis-related genes and Wnt/β-catenin signal pathway (P < 0.05). The present study identified that SLP-2 may predict a poor prognosis in CRC patients as a novel marker, and SLP-2 may facilitate the migration and invasion of CRC via regulating Wnt/β-catenin pathway activities.