66 Biomed Environ Sci, 2021; 34(1): 66-70 Letter to the Editor Potential Function of MMP3 Gene in Degradation of Extracellular Matrix Complex in Colorectal Carcinoma* DAI Xiao Yong1,&, SONG An Yi1,2,&, MU Lan1, WANG Li Jun1, and HUANG Lai Qiang1,2,# Colorectal cancer (CRC) is a kind of malignant language software through special packages such as tumor that occurs in the digestive tract. CRC occurs bioconductors and limma[2]. In addition, analysis of globally and has high rates of morbidity and down-regulated genes may reveal functional defects mortality. Its incidence and mortality are second and mutations that trigger the occurrence of cancer. only to gastric cancer, esophageal cancer, and Meanwhile, over-expressed genes may be useful as primary liver cancer in digestive system biomarkers in the clinic or to identify potential malignancies. Most CRC cases are adenomas. A few antigen targets. Analysis using conventional are squamous epithelial cancers, which can spread methods, such as enrichment analysis and protein- to adjacent tissues and organs through lymph and protein interaction (PPI) networks, analysis of blood circulation, or directly. The occurrence of CRC differentially expressed genes (DEGs) may provide a is related to factors that include gene mutation, novel approach to reveal significant genes and dietary habits, family disease history, smoking, signaling pathways related to disease. drinking, and external carcinogens. Diagnostic Based on special experimental processing methods for CRC mainly include digital rectal conditions and uniform statistical method of examination, X-ray barium enema, sigmoidoscopy, samples, the refined GAE110224 gene chips were and fiber colonoscopy. However, low sensitivity of chosen for this study from the GEO database. The detection is a problem, and false positives still occur. original GSE110224 gene chip contains information Thus, screening for specific over-expressed genes as on gene expression in CRC tissue and normal tissue biomarkers is meaningful in the clinic for diagnosis. from 17 patients treated clinically. In total, 36,951 Additionally, several reports have discussed DEGs were identified. Of these, 20,006 that were molecular mechanisms associated with the over-expressed and 16,945 that were down- occurrence of CRC, such as the K-Ras and p53 regulated were included. By setting with the signaling pathways. The crucial pathways have not parameters |logFC| > 2 and P < 0.05, 71 markedly been identical. Data of clinical samples from over-expressed and 106 markedly down-regulated bioinformatics databases with information of gene genes were screened. The volcano map of DEGs expression on a large scale may reveal significant from the downloaded document was drawn using pathways that are involved in cancer development[1]. Prism 8 software (Figure 1). The top ten over- The Gene Expression Omnibus (GEO) database expressed genes according to value of log (fold includes information acquired globally using many change) expression levels are listed in gene chips. The data include clinically relevant Supplementary Table S1 available in www. expression of genes and several types of RNA, besjournal.com. including messenger RNA (mRNA), micro RNA In addition to the aforementioned GEO database, (miRNA), and long noncoding RNA (lncRNA), and online platforms including Gene Expression Profiling data of DNA methylation. Clinical data can be Interactive Analysis (GEPIA) and OncoLnc can be downloaded from the website and visualized by R useful to visualize gene expression and survival doi: 10.3967/bes2021.009 *This work was supported with funding awarded to LH from the National Natural Science Foundation of China (NSFC) [81872368]; Shenzhen Science Technology and Innovation Commission Key Projects [JCYJ20180508152130899]; State Key Lab Construction Project (GuoKeFaJi [2018]38); and Shenzhen Development and Reform Commission Subject Construction Project [2017]1434. 1. Shenzhen Key Laboratory of Gene and Antibody Therapy, Center for Biotechnology and Biomedicine, State Key Laboratory of Chemical Oncogenomics, Tsinghua-Berkeley Shenzhen Institute (TBSI), Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong, China; 2. Department of Chemistry, Tsinghua University, Beijing 100084, China Function of MMP3 in colorectal cancer 67 curves based on clinical data from The Cancer besjournal.com). In addition, MMP3 and CXCL5 were Genome Atlas (TCGA) website. The Human Protein comparatively over-expressed in CRC tissue with Atlas database contains a variety of immune- significant differences. These genes could be histochemical patches for significant genes in several potential biomarkers for diagnosis in clinical settings types of cancer tissues and normal tissues. based on the high accuracy of their ROC curves as Functional protein association networks (STRING) is reported. an online platform for the analysis of gene Survival analysis revealed log-rank P values of enrichment and PPI. The Functional Annotation 0.0106, 0.0051, 0.1552, and 0.2861 for MMP3, Bioinformatics Microarray Analysis (DAVID) website TIMP1, KRT80, and CXCL5, respectively is useful for Gene Ontology enrichment analyses of (Supplementary Figure S3 available in www. DEGs identified from gene chips. Presently, the besjournal.com). Therefore, expression of MMP3 functions and involved signaling pathways of and TIMP1 might be closely associated with patient significant genes were searched from GeneCards and survival. In particular, the MMP3 gene is important the Kyoto Encyclopedia of Genes and Genomes for collagen degradation, extracellular matrix (ECM) website for further demonstration. Volcano maps of structure, wound repair, and tissue remodeling. It is DEGs, expression histograms, survival curves, and closely related to cancer occurrence and cancer cell receiver operating characteristic (ROC) curves were migration. The TIMP1 protein is an inhibitor of plotted using Prism 8 software. Bubble charts of matrix metallopeptidase and has a negative pathway enrichment were constructed using R 3.6.3 relationship with MMP3. Immunohistochemical software based on the results of enrichment analysis examinations of pathological and normal tissues from the DAVID website[3]. revealed less frequent gene expression of TIMP1, Based on a survey of relevant reports, four genes while MMP3 gene expression in CRC tissues was (MMP3, TIMP1, KRT80, and CXCL5) with high levels comparatively increased. The findings were of expression and significant differences were consistent with the analysis results from the GEO selected for further analysis as shown in and TCGA databases (Supplementary Figure S4 Supplementary Figure S1 available in www. available in www.besjournal.com). Thus, MMP3 was besjournal.com. The area under the ROC curve for implicated as being functionally important in the MMP3, TIMP1, KRT80, and CXCL5 was 0.8616, development of CRC. 0.9308, 0.9204, and 0.8062, respectively Concerning DEGs, 71 markedly over-expressed (Supplementary Figure S2 available in www. genes were selected for enrichment analysis using the parameters of logFC > 2 and P < 0.05. PPI Genes network and pathway enrichment were performed 8 [4] TIMP1 using the STRING website (Figure 2) . Processes KRT80 related to chemokine receptors CXCL1, CXCL5, and 6 MMP3 CXCL11, and the function of ECM related to matrix AQP8 value) CA4 metalloproteinase (MMPs) were relatively P CA1 4 CXCL5 concentrated from PPI network. In addition, the MS4A12 MMP1, MMP3, MMP7, and MMP10 were located in CLCA4 −log10 ( the kernel of the PPI network, and so may be 2 influential on the development of CRC. We also imported 71 markedly over-expressed genes into the 0 DAVID website for enrichment analysis. The genes 0 2 4 6 −6 −4 −2 included those associated with important signaling logFC pathways of biological process, molecular functions, Figure 1. Volcano map of differentially and cellular components. The results were analyzed [5] expressed genes. The X-axis displays values of and visualized with R language software (Figure 3) . −logFC for each gene. The y-axis displays the Generally, the processes of inflammatory −log10 (P value). Genes with positive logFC are response, immune response, collagen catabolic over-expressed, and genes with negative logFC process, chemokine-mediated signaling pathway, are down-regulated. Four remarkably over- cell-cell signaling, and chemotaxis were more expressed and significantly down-regulated concentrated in the enrichment analysis. In addition, genes are denoted in red and blue, the enrichment analysis revealed the association of respectively. the processes of extracellular matrix organization, 68 Biomed Environ Sci, 2021; 34(1): 66-70 extracellular matrix disassembly, and collagen fibril The MMP family of proteins are involved in the organization with the MMP3 gene according to a breakdown of the extracellular matrix during disease previous survey from the Genecards website. As processes, such as arthritis and cancer metastasis[7]. reported, MMPs has appreciable impacts on collagen MMP3 is a zinc-dependent endopeptidase that can degradation, maintenance of the structure of the degrade several extracellular components and extracellular matrix, tissue remodeling, wound molecules, including transferrin, laminin, collagen, healing, and cancer migration, which may play a and chondroitin. The extracellular matrix is mainly significant role in the development of colorectal composed of collagen, elastin, proteoglycans, and cancer according to PPI network